Hatena::Groupbioruby

"aac".translate #=> "N" このページをアンテナに追加 RSSフィード

2008-01-10

H-InvDB REST web service client class added

|  H-InvDB REST web service client class added - "aac".translate #=> "N" を含むブックマーク はてなブックマーク -  H-InvDB REST web service client class added - "aac".translate #=> "N"  H-InvDB REST web service client class added - "aac".translate #=> "N" のブックマークコメント

Katayama-san commited a new IO class Bio::Hinv to access the H-InvDB REST web service.

H-InvDB web service provides 12 APIs.

acc2hit - HIT ID of accession number

URI:

Output:

<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
        <H-INVITATIONAL-ID>HIT000053961</H-INVITATIONAL-ID>
</H-Inv>

In bioruby,

irb(main):001:0> require 'bio'
irb(main):002:0> Bio::Hinv.acc2hit("BC053657")
=> "HIT000053961"

hit2acc - Accession No of HIT ID

URI:

Output:

<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
        <ACCESSION-NO>AK097327</ACCESSION-NO>
</H-Inv>% 

In bioruby:

irb(main):003:0> Bio::Hinv.hit2acc("HIT000022181") 
=> "AK097327"

hit_cnt - total number of HIT ID

URI:

Output:

<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
        <TRANSCRIPT_CNT>187156</TRANSCRIPT_CNT>
</H-Inv>

The last line don't have return code.

In bioruby:

irb(main):004:0> Bio::Hinv.hit_cnt 
=> 187156

hit_definition - HIT definition of HIT ID

URI:

Output:

<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
        <HIT_FUNCTION>
                <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
                <DATA-SOURCE_DEFINITION>Rho guanine nucleotide exchange factor 10.</DATA-SOURCE_DEFINITION>
                <CDNA_REP-H-INVITATIONAL>Representative transcript</CDNA_REP-H-INVITATIONAL>
                <CDNA_SPLICING-ISOFORM_CURATION></CDNA_SPLICING-ISOFORM_CURATION>
                <DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>NP_055444</DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>
                <DATA-SOURCE_IDENTITY>100.0</DATA-SOURCE_IDENTITY>
                <DATA-SOURCE_COVERAGE>100.0</DATA-SOURCE_COVERAGE>
                <DATA-SOURCE_HOMOLOGOUS_SPECIES>Homo sapiens</DATA-SOURCE_HOMOLOGOUS_SPECIES>
                <DATA-SOURCE_SIMILARITY-CATEGORY>Identical to known human protein(Category I).</DATA-SOURCE_SIMILARITY-CATEGORY>
        </HIT_FUNCTION>
</H-Inv>

In bioruby:

simple access

irb(main):006:0> Bio::Hinv.hit_definition("HIT000000001") 
=> "Rho guanine nucleotide exchange factor 10."

and full access

irb(main):007:0> serv = Bio::Hinv::HitDefinition.new
irb(main):008:0> serv.query("hit" => "HIT000000001")
irb(main):009:0> serv.result
=> "Rho guanine nucleotide exchange factor 10."
irb(main):010:0> serv.data_source_definition
=> "Rho guanine nucleotide exchange factor 10."
irb(main):011:0> serv.cdna_rep_h_invitational
=> "Representative transcript"
irb(main):012:0> serv.cdna_splicing_isoform_curation
=> nil
irb(main):013:0> serv.data_source_db_reference_protein_motif_id
=> "NP_055444"
irb(main):014:0> serv.data_source_identity
=> 100.0
irb(main):015:0> serv.data_source_coverage
=> 100.0
irb(main):016:0> serv.data_source_homologous_species
=> "Homo sapiens"
irb(main):017:0> serv.data_source_similarity_category
=> "Identical to known human protein(Category I)."

hit_pubmedid - PMID of HIT ID

URI:

Output:

<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
<CDNA_DB-REFERENCE_PUBMED>7624364</CDNA_DB-REFERENCE_PUBMED>
<CDNA_DB-REFERENCE_PUBMED>11279095</CDNA_DB-REFERENCE_PUBMED>
<CDNA_DB-REFERENCE_PUBMED>15489334</CDNA_DB-REFERENCE_PUBMED>
</H-Inv>

In bioruby:

irb(main):031:0> Bio::Hinv.hit_pubmedid("HIT000053961")
=> [7624364, 11279095, 15489334]

hit_xml - HIT XML file of HIT ID

URI:

Output:

<?xml version="1.0" standalone="yes" ?>
<H-Inv>
  <cDNAXML>
    <CLUSTER-ID>HIX0021591</CLUSTER-ID>
    <CLUSTER-ID-VERSION>HIX0021591.11</CLUSTER-ID-VERSION>
    <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
    <H-INVITATIONAL-ID-VERSION>HIT000000001.11</H-INVITATIONAL-ID-VERSION>
    <ACCESSION-NO>AB002292</ACCESSION-NO>
    <ACCESSION-NO-VERSION>AB002292.2</ACCESSION-NO-VERSION>
    <GENOME-STATISTICS>build 36.2</GENOME-STATISTICS>
    <DIVISION>HUM</DIVISION>
    <MOL-TYPE>mRNA</MOL-TYPE>
    <CDNA_DATE-CREATE>14-Feb-2004</CDNA_DATE-CREATE>
    <CDNA_DATE-LAST-UPDATE>26-Dec-2007</CDNA_DATE-LAST-UPDATE>
    <CDNA_DATE-LAST-MODIFIED>26-Dec-2007</CDNA_DATE-LAST-MODIFIED>
    <CDNA_H-INV-DB-RELEASE>5.0</CDNA_H-INV-DB-RELEASE>
    <HIT-RELEASE>5.0</HIT-RELEASE>
    <CDNA_DATE-ANNOTATION-LAST-UPDATE>26-Dec-2007</CDNA_DATE-ANNOTATION-LAST-UPDATE>
    <CDNA_DATE-ANNOTATION-LAST-MODIFIED>26-Dec-2007</CDNA_DATE-ANNOTATION-LAST-MODIFIED>
    <HIT-ANNOTATION-RELEASE>5.0</HIT-ANNOTATION-RELEASE>
    <CHROMOSOME-NUMBER>8</CHROMOSOME-NUMBER>
    <CHROMOSOME-BAND>8p23.3</CHROMOSOME-BAND>
    <CDNA_START>1759549</CDNA_START>
    <CDNA_END>1894206</CDNA_END>
    <CDNA_STRAND>+</CDNA_STRAND>
    <CDNA_LOCUS_START>1</CDNA_LOCUS_START>
    <CDNA_LOCUS_END>134658</CDNA_LOCUS_END>
    <CDNA_DB-REFERENCE_KEGG-GENES>9639</CDNA_DB-REFERENCE_KEGG-GENES>
    <CDNA_DB-REFERENCE_ENSEMBL>ENST00000262112</CDNA_DB-REFERENCE_ENSEMBL>
    <CDNA_DB-REFERENCE_ENSEMBL>ENST00000349830</CDNA_DB-REFERENCE_ENSEMBL>
    <CDNA_DB-REFERENCE_ENSEMBL>ENST00000382794</CDNA_DB-REFERENCE_ENSEMBL>
    <CDNA_DB-REFERENCE_ENSEMBL>ENST00000382795</CDNA_DB-REFERENCE_ENSEMBL>
    <CDNA_DB-REFERENCE_ENTREZGENE>9639</CDNA_DB-REFERENCE_ENTREZGENE>
    <CDNA_DB-REFERENCE_CCDS>CCDS34794</CDNA_DB-REFERENCE_CCDS>
    <CDNA_DB-REFERENCE_REFSEQ>NM_014629</CDNA_DB-REFERENCE_REFSEQ>
    <CDNA_REP-H-INVITATIONAL>Representative transcript</CDNA_REP-H-INVITATIONAL>
    <CDNA_SPLICE-ACCEPTOR>CAGAAG</CDNA_SPLICE-ACCEPTOR>
    <CDNA_SPLICE-ACCEPTOR>CAGCAG</CDNA_SPLICE-ACCEPTOR>
    <CDNA_SPLICE-ACCEPTOR>CAGGAG</CDNA_SPLICE-ACCEPTOR>
    <CDNA_H-INVITATIONAL-PROTEIN-ID>HIP000042367</CDNA_H-INVITATIONAL-PROTEIN-ID>
    <CDNA_H-INVITATIONAL-PROTEIN-ID-VERSION>HIP000042367.1</CDNA_H-INVITATIONAL-PROTEIN-ID-VERSION>
    <CDNA_DB-REFERENCE_REFSEQ-PROTEIN-ID>NP_055444</CDNA_DB-REFERENCE_REFSEQ-PROTEIN-ID>
    <JOURNAL_DB-REFERENCE_MEDLINE>15103394</JOURNAL_DB-REFERENCE_MEDLINE>
    <MRNA-INSPECTION>
      <CLONE-NUMBER_ORIGINAL>hf00223s1</CLONE-NUMBER_ORIGINAL>
      <TISSUE-TYPE-ORIGIN_ORIGINAL>brain</TISSUE-TYPE-ORIGIN_ORIGINAL>
      <DATA-PROVIDER>KDRI</DATA-PROVIDER>
      <LENGTH-OF-CDNA_ORIGINAL>5589</LENGTH-OF-CDNA_ORIGINAL>
      <NUMBER-OF-EXON_ORIGINAL>29</NUMBER-OF-EXON_ORIGINAL>
      <NUMBER-OF-A_ORIGINAL>1495</NUMBER-OF-A_ORIGINAL>
      <NUMBER-OF-T_ORIGINAL>1244</NUMBER-OF-T_ORIGINAL>
      <NUMBER-OF-G_ORIGINAL>1467</NUMBER-OF-G_ORIGINAL>
      <NUMBER-OF-C_ORIGINAL>1383</NUMBER-OF-C_ORIGINAL>
    </MRNA-INSPECTION>
    <PATHOLOGY>
      <PATHOLOGY_DATE-LAST-UPDATE>26-Dec-2007</PATHOLOGY_DATE-LAST-UPDATE>
      <PATHOLOGY_DATE-LAST-MODIFIED>31-Mar-2003</PATHOLOGY_DATE-LAST-MODIFIED>
      <PATHOLOGY_DISEASE-RELEASE>5.0</PATHOLOGY_DISEASE-RELEASE>
      <KNOWN-DISEASE-GENE>
        <CDNA-OMIM_DB-REFERENCE_OMIM-DISEASE>608236</CDNA-OMIM_DB-REFERENCE_OMIM-DISEASE>
        <CDNA-OMIM_DISEASE_DISEASE-NAME>Slowed nerve conduction velocity, AD</CDNA-OMIM_DISEASE_DISEASE-NAME>
        <CDNA-OMIM_DB-REFERENCE_OMIM>608136</CDNA-OMIM_DB-REFERENCE_OMIM>
        <CDNA-OMIM_MORBID-MAP_OMIM-TITLE>RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 10</CDNA-OMIM_MORBID-MAP_OMIM-TITLE>
      </KNOWN-DISEASE-GENE>
      <ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>148370</ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>
      <ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>606129</ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>
      <ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>606662</ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>
      <ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>609259</ORPHAN-DISEASE_DB-REFERENCE_LOCUS-OMIM>
    </PATHOLOGY>
    <EVOLUTIONARY-FEATURE>
      <EVOLUTIONARY-FEATURE_DATE-LAST-UPDATE>26-Dec-2007</EVOLUTIONARY-FEATURE_DATE-LAST-UPDATE>
      <EVOLUTIONARY-FEATURE_DATE-LAST-MODIFIED>26-Dec-2007</EVOLUTIONARY-FEATURE_DATE-LAST-MODIFIED>
      <EVOLUTIONARY-FEATURE_EVOLUTION-RELEASE>5.0</EVOLUTIONARY-FEATURE_EVOLUTION-RELEASE>
      <ORTHOLOGY>
        <ACCESSION-NO>AK147669</ACCESSION-NO>
        <SPECIES>Mus musculus (Mouse)</SPECIES>
        <MGI-ID>MGI:3573648</MGI-ID>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>BC059220</ACCESSION-NO>
        <SPECIES>Mus musculus (Mouse)</SPECIES>
        <MGI-ID>MGI:1920004</MGI-ID>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>BC114112</ACCESSION-NO>
        <SPECIES>Bos taurus (Cow)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>CR391701</ACCESSION-NO>
        <SPECIES>Gallus gallus (Chicken)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>ENSCAFT00000024924</ACCESSION-NO>
        <SPECIES>Canis familiaris (Dog)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>ENSORLT00000021592</ACCESSION-NO>
        <SPECIES>Oryzias Latipes (Medaka)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>ENSRNOT00000016745</ACCESSION-NO>
        <SPECIES>Rattus norvegicus (Rat)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>GSTENT00032455001</ACCESSION-NO>
        <SPECIES>Tetraodon nigroviridis (Tetraodon)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>SINFRUT00000172682</ACCESSION-NO>
        <SPECIES>Takifugu rubripes (Fugu)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>XM_001343066</ACCESSION-NO>
        <SPECIES>Danio rerio (Zebrafish)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>XM_001381452</ACCESSION-NO>
        <SPECIES>Monodelphis domestica (Opossum)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>XM_001488501</ACCESSION-NO>
        <SPECIES>Equus caballus (Horse)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>XM_528056</ACCESSION-NO>
        <SPECIES>Pan troglodytes (Chimpanzee)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>XM_680636</ACCESSION-NO>
        <SPECIES>Danio rerio (Zebrafish)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>XM_680883</ACCESSION-NO>
        <SPECIES>Danio rerio (Zebrafish)</SPECIES>
      </ORTHOLOGY>
      <ORTHOLOGY>
        <ACCESSION-NO>XM_846774</ACCESSION-NO>
        <SPECIES>Canis familiaris (Dog)</SPECIES>
      </ORTHOLOGY>
    </EVOLUTIONARY-FEATURE>
    <CDNA-INFO>
      <SNP>
        <SNP_START>325</SNP_START>
        <SNP_END>325</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs4875950</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>A/C</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Pro47Pro]</SNP_TRANSLATION>
        <SNP_STRAND>-</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>571</SNP_START>
        <SNP_END>571</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs749822</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>A/G</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Val129Val]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>775</SNP_START>
        <SNP_END>775</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2272708</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Ala197Ala]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>814</SNP_START>
        <SNP_END>814</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs7003969</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>G/A</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Glu210Glu]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>1294</SNP_START>
        <SNP_END>1294</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs9657362</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>G/C</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Leu370Phe]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>1297</SNP_START>
        <SNP_END>1297</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs34655804</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Phe371Phe]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>1615</SNP_START>
        <SNP_END>1615</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs3758004</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Phe477Phe]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>1831</SNP_START>
        <SNP_END>1831</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs12681485</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Leu549Leu]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>1938</SNP_START>
        <SNP_END>1938</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs1045489</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>G/A</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Arg585Lys]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2175</SNP_START>
        <SNP_END>2175</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs34319003</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>T/C</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Met664Thr]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2239</SNP_START>
        <SNP_END>2239</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2294038</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>T/C</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Tyr685Tyr]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2282</SNP_START>
        <SNP_END>2282</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2294039</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>G/A</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Val700Ile]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2287</SNP_START>
        <SNP_END>2287</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2294040</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[His701His]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2569</SNP_START>
        <SNP_END>2569</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs34036746</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Asp795Asp]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2764</SNP_START>
        <SNP_END>2764</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2272613</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Pro860Pro]</SNP_TRANSLATION>
        <SNP_STRAND>-</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2920</SNP_START>
        <SNP_END>2920</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2272611</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Ile912Ile]</SNP_TRANSLATION>
        <SNP_STRAND>-</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>2939</SNP_START>
        <SNP_END>2939</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs35354057</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>A/C</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Thr919Pro]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>3093</SNP_START>
        <SNP_END>3093</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs35925274</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Thr970Met]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>3134</SNP_START>
        <SNP_END>3134</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs17683288</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>T/G</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Ser984Ala]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>3200</SNP_START>
        <SNP_END>3200</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2272610</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>A/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Thr1006Ser]</SNP_TRANSLATION>
        <SNP_STRAND>-</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>3232</SNP_START>
        <SNP_END>3233</SNP_END>
        <SNP_LOCATION-TYPE>^</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs35849152</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>-/G</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>3598</SNP_START>
        <SNP_END>3598</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2272609</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>G/A</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Ser1138Ser]</SNP_TRANSLATION>
        <SNP_STRAND>-</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>3622</SNP_START>
        <SNP_END>3622</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs2272608</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[His1146His]</SNP_TRANSLATION>
        <SNP_STRAND>-</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>3922</SNP_START>
        <SNP_END>3922</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs3735876</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>G/A</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Synonymous[Ser1246Ser]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>4157</SNP_START>
        <SNP_END>4157</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs35095003</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>C/T</SNP_BASE-CDNA>
        <SNP_LOCATION>CDS</SNP_LOCATION>
        <SNP_TRANSLATION>Nonsynonymous[Pro1325Ser]</SNP_TRANSLATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>4518</SNP_START>
        <SNP_END>4518</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs6558566</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>A/G</SNP_BASE-CDNA>
        <SNP_LOCATION>3'UTR</SNP_LOCATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>4613</SNP_START>
        <SNP_END>4613</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs6991392</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>A/G</SNP_BASE-CDNA>
        <SNP_LOCATION>3'UTR</SNP_LOCATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>5420</SNP_START>
        <SNP_END>5420</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs14375</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>T/G</SNP_BASE-CDNA>
        <SNP_LOCATION>3'UTR</SNP_LOCATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <SNP>
        <SNP_START>5499</SNP_START>
        <SNP_END>5499</SNP_END>
        <SNP_LOCATION-TYPE>..</SNP_LOCATION-TYPE>
        <SNP_DB-REFERENCE_DBSNP>rs11986753</SNP_DB-REFERENCE_DBSNP>
        <SNP_BASE-CDNA>T/C</SNP_BASE-CDNA>
        <SNP_LOCATION>3'UTR</SNP_LOCATION>
        <SNP_STRAND>+</SNP_STRAND>
      </SNP>
      <EXON-CDNA>
        <EXON-CDNA_START>1</EXON-CDNA_START>
        <EXON-CDNA_END>137</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>138</EXON-CDNA_START>
        <EXON-CDNA_END>221</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>222</EXON-CDNA_START>
        <EXON-CDNA_END>377</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>378</EXON-CDNA_START>
        <EXON-CDNA_END>665</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>666</EXON-CDNA_START>
        <EXON-CDNA_END>729</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>730</EXON-CDNA_START>
        <EXON-CDNA_END>806</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>807</EXON-CDNA_START>
        <EXON-CDNA_END>863</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>864</EXON-CDNA_START>
        <EXON-CDNA_END>1027</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1028</EXON-CDNA_START>
        <EXON-CDNA_END>1144</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1145</EXON-CDNA_START>
        <EXON-CDNA_END>1259</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1260</EXON-CDNA_START>
        <EXON-CDNA_END>1366</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1367</EXON-CDNA_START>
        <EXON-CDNA_END>1444</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1445</EXON-CDNA_START>
        <EXON-CDNA_END>1624</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1625</EXON-CDNA_START>
        <EXON-CDNA_END>1741</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1742</EXON-CDNA_START>
        <EXON-CDNA_END>1834</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>1835</EXON-CDNA_START>
        <EXON-CDNA_END>2005</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2006</EXON-CDNA_START>
        <EXON-CDNA_END>2151</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2152</EXON-CDNA_START>
        <EXON-CDNA_END>2327</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2328</EXON-CDNA_START>
        <EXON-CDNA_END>2443</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2444</EXON-CDNA_START>
        <EXON-CDNA_END>2571</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2572</EXON-CDNA_START>
        <EXON-CDNA_END>2672</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2673</EXON-CDNA_START>
        <EXON-CDNA_END>2794</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2795</EXON-CDNA_START>
        <EXON-CDNA_END>2881</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>2882</EXON-CDNA_START>
        <EXON-CDNA_END>3105</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>3106</EXON-CDNA_START>
        <EXON-CDNA_END>3263</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>3264</EXON-CDNA_START>
        <EXON-CDNA_END>3406</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>3407</EXON-CDNA_START>
        <EXON-CDNA_END>3581</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>3582</EXON-CDNA_START>
        <EXON-CDNA_END>3704</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-CDNA>
        <EXON-CDNA_START>3705</EXON-CDNA_START>
        <EXON-CDNA_END>5589</EXON-CDNA_END>
      </EXON-CDNA>
      <EXON-GENOME>
        <EXON-GENOME_START>1759549</EXON-GENOME_START>
        <EXON-GENOME_END>1759686</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1778926</EXON-GENOME_START>
        <EXON-GENOME_END>1779009</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1793533</EXON-GENOME_START>
        <EXON-GENOME_END>1793688</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1795470</EXON-GENOME_START>
        <EXON-GENOME_END>1795757</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1799946</EXON-GENOME_START>
        <EXON-GENOME_END>1800009</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1802099</EXON-GENOME_START>
        <EXON-GENOME_END>1802175</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1804767</EXON-GENOME_START>
        <EXON-GENOME_END>1804823</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1812144</EXON-GENOME_START>
        <EXON-GENOME_END>1812307</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1815621</EXON-GENOME_START>
        <EXON-GENOME_END>1815737</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1818208</EXON-GENOME_START>
        <EXON-GENOME_END>1818322</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1821174</EXON-GENOME_START>
        <EXON-GENOME_END>1821280</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1829142</EXON-GENOME_START>
        <EXON-GENOME_END>1829219</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1829966</EXON-GENOME_START>
        <EXON-GENOME_END>1830145</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1831906</EXON-GENOME_START>
        <EXON-GENOME_END>1832022</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1834006</EXON-GENOME_START>
        <EXON-GENOME_END>1834098</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1838854</EXON-GENOME_START>
        <EXON-GENOME_END>1839024</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1841144</EXON-GENOME_START>
        <EXON-GENOME_END>1841289</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1844868</EXON-GENOME_START>
        <EXON-GENOME_END>1845043</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1858537</EXON-GENOME_START>
        <EXON-GENOME_END>1858652</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1859041</EXON-GENOME_START>
        <EXON-GENOME_END>1859168</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1859347</EXON-GENOME_START>
        <EXON-GENOME_END>1859447</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1860856</EXON-GENOME_START>
        <EXON-GENOME_END>1860977</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1861950</EXON-GENOME_START>
        <EXON-GENOME_END>1862036</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1864000</EXON-GENOME_START>
        <EXON-GENOME_END>1864223</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1864859</EXON-GENOME_START>
        <EXON-GENOME_END>1865016</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1869373</EXON-GENOME_START>
        <EXON-GENOME_END>1869515</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1881054</EXON-GENOME_START>
        <EXON-GENOME_END>1881228</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1888278</EXON-GENOME_START>
        <EXON-GENOME_END>1888400</EXON-GENOME_END>
      </EXON-GENOME>
      <EXON-GENOME>
        <EXON-GENOME_START>1892322</EXON-GENOME_START>
        <EXON-GENOME_END>1894206</EXON-GENOME_END>
      </EXON-GENOME>
    </CDNA-INFO>
    <SEQUENCE>
      <NUCLEOTIDE_ORIGINAL>GGGGTCGCGGGGGACGCGGGGGACGCGGGGGACGCGGGGGACGGCGGGGAACGGCGGGGAACAGCGGGGGACGGCGGGGAACAGCGGGGGACGGCGGGGAACAGCAGGGGACTGCGGGTCGCGTCCTGGCCGCCGAGGAGCTCCTTCCCTTAACAGAGCTGAGAGAGGCATCTGGAGCTGCAGCATGGACCAGCGAGAGCCCCTGCCTCCCGCTCCTGCAGAAAATGAAATGAAATATGATACCAATAATAATGAAGAGGAAGAGGGAGAACAGTTCGATTTTGACAGTGGAGATGAAATCCCAGAAGCGGACAGACAGGCCCCATCCGCCCCTGAGACAGGAGGTGCTGGAGCCAGTGAAGCCCCTGCACCCACAGGAGGTGAGGATGGAGCTGGAGCAGAAACCACCCCAGTGGCAGAGCCTACTAAGCTGGTGCTCCCGATGAAAGTCAACCCATATTCTGTCATCGACATCACGCCATTCCAGGAGGACCAGCCGCCCACCCCCGTGCCCAGCGCTGAGGAGGAGAATGTGGGTCTCCATGTGCCCTGCGGGTACTTGGTGCCTGTACCCTGCGGCTATGCGGTGCCCTCCAACCTGCCCCTCCTGCTGCCCGCCTACTCCAGCCCGGTCATCATCTGCGCCACGTCCCTGGACGAAGAAGAAACACCAGAAGTCACAGAAGATCGCCAGCCCAATTCTCTGAGTTCCGAGGAGCCTCCAACCAGTGAAGATCAAGTCGGTCGAGAGGACAGCGCACTTGCCCGCTGGGCCGCAGACCCGGCCAACACAGCCTGGATGGAGAATCCAGAGGAAGCAATTTACGATGACGTTCCAAGGGAAAACTCAGACTCTGAACCAGATGAAATGATTTATGATGATGTTGAGAATGGGGATGAAGGTGGAAACAGCTCCTTGGAATACGGATGGAGTTCGAGTGAATTTGAAAGTTACGAAGAGCAGAGTGACTCGGAGTGCAAGAATGGGATTCCCAGGTCCTTCCTGCGCAGCAACCACAAAAAGCAACTTTCTCATGACCTAACCCGTTTAAAGGAGCACTATGAGAAAAAGATGAGAGATTTGATGGCAAGCACGGTGGGCGTGGTGGAGATTCAGCAGCTCAGGCAGAAGCATGAACTGAAGATGCAGAAGCTCGTGAAGGCCGCGAAGGACGGCACCAAGGACGGGCTGGAGAGGACCAGGGCAGCCGTGAAGAGGGGCCGCTCCTTCATCAGGACCAAGTCTCTCATCGCACAGGATCACAGATCTTCTCTTGAGGAAGAACAGAATTTGTTCATTGATGTTGACTGCAAGCACCCGGAAGCCATCTTGACCCCGATGCCCGAGGGTTTATCTCAGCAGCAGGTTGTAAGAAGATATATACTGGGTTCAGTTGTCGACAGTGAAAAGAACTACGTAGATGCTCTTAAGAGGATTTTGGAGCAATATGAGAAGCCGCTGTCTGAGATGGAGCCAAAGGTTCTGAGTGAGAGGAAGCTGAAGACGGTGTTCTACCGAGTCAAAGAGATCCTGCAGTGCCACTCGCTATTTCAGATCGCGCTGGCCAGCCGCGTTTCCGAGTGGGACTCCGTGGAAATGATAGGCGATGTCTTCGTGGCTTCGTTTTCTAAGTCCATGGTGCTGGATGCATACAGTGAATATGTGAACAATTTCAGCACAGCCGTGGCAGTCCTCAAGAAAACATGTGCCACAAAGCCCGCTTTTCTTGAATTTTTAAAGCAGGAACAGGAGGCCAGCCCCGATCGAACCACGCTCTACAGCCTGATGATGAAGCCCATCCAGAGGTTCCCACAGTTCATCCTCCTGCTCCAGGACATGCTGAAGAACACCTCCAAAGGCCACCCCGACAGGCTGCCTCTTCAGATGGCCCTGACAGAGCTCGAAACACTAGCAGAGAAGTTAAATGAAAGAAAGAGAGATGCTGATCAACGCTGTGAAGTGAAGCAAATAGCCAAAGCCATAAACGAAAGATACCTGAACAAGCTTCTCAGCAGTGGAAGCCGATACCTCATTCGATCAGATGATATGATAGAAACAGTTTACAACGACAGAGGAGAGATTGTTAAAACCAAAGAACGCCGAGTCTTCATGTTAAATGATGTGTTAATGTGTGCCACCGTCAGCTCACGCCCCTCTCATGACAGCCGTGTGATGAGCAGCCAGAGGTACTTGCTGAAGTGGAGCGTTCCACTGGGACATGTGGACGCCATCGAGTATGGCAGCAGCGCAGGCACGGGCGAGCACAGCAGGCACCTTGCCGTTCACCCGCCGGAGAGCCTGGCCGTGGTTGCTAACGCGAAACCAAACAAAGTTTACATGGGGCCAGGACAACTGTATCAAGATTTACAAAACTTGTTGCATGACTTAAATGTAATTGGCCAAATCACTCAGCTGATAGGAAACCTTAAAGGAAACTATCAGAACTTAAACCAGTCAGTAGCCCATGACTGGACATCAGGTTTACAAAGGCTTATTTTGAAGAAAGAAGATGAAATCAGAGCTGCGGACTGCTGCAGAATTCAGTTACAGCTTCCCGGGAAGCAGGACAAATCTGGGCGACCGACGTTCTTTACAGCTGTGTTCAATACGTTCACCCCTGCCATCAAGGAGTCCTGGGTCAACAGCTTACAGATGGCCAAGCTCGCCCTAGAAGAGGAGAACCACATGGGCTGGTTCTGTGTGGAAGACGATGGGAATCACATTAAAAAGGAGAAGCATCCTCTCCTCGTCGGACACATGCCCGTGATGGTGGCCAAGCAGCAGGAGTTCAAGATTGAATGTGCTGCTTATAACCCTGAACCTTACCTAAATAATGAAAGCCAGCCAGATTCATTTTCCACGGCACATGGTTTCCTGTGGATCGGAAGTTGCACCCATCAAATGGGTCAGATTGCCATCGTCTCGTTTCAAAATTCCACTCCCAAAGTCATTGAGTGCTTCAACGTGGAATCTCGCATCCTGTGCATGCTGTACGTTCCCGTCGAGGAGAAGCGCAGAGAGCCTGGGGCACCCCCGGACCCCGAGACCCCGGCCGTGAGAGCTTCTGATGTCCCCACGATCTGTGTAGGGACGGAGGAGGGAAGCATTTCCATTTATAAAAGCAGTCAAGGCTCCAAGAAAGTGAGACTTCAGCACTTTTTCACTCCTGAGAAGTCCACAGTCATGAGCCTGGCTTGCACGTCTCAGAGCCTGTACGCTGGCCTGGTCAACGGGGCAGTCGCCAGCTACGCCAGAGCCCCAGATGGATCCTGGGATTCAGAACCTCAAAAAGTGATCAAGTTAGGCGTCCTACCAGTTAGAAGTCTACTCATGATGGAAGACACGTTGTGGGCGGCTTCCGGAGGTCAAGTCTTCATCATCAGTGTGGAGACTCATGCTGTAGAGGGTCAGCTGGAGGCCCACCAGGAGGAAGGCATGGTGATCTCCCACATGGCCGTGTCCGGCGTCGGGATCTGGATTGCCTTCACCTCAGGGTCCACGCTCCGCCTTTTTCACACGGAAACTCTCAAGCACCTGCAGGACATCAACATCGCCACCCCTGTTCACAACATGCTGCCAGGGCACCAGCGGCTGTCGGTGACGAGCCTGCTCGTCTGCCACGGATTGCTGATGGTCGGCACCAGCCTGGGAGTCCTCGTGGCCCTGCCGGTCCCACGTCTGCAAGGGATTCCCAAAGTGACCGGAAGAGGCATGGTCTCCTACCATGCACACAACAGTCCTGTCAAATTCATCGTCCTGGCCACGGCTCTGCACGAGAAAGACAAGGACAAATCCAGGGACAGCCTGGCTCCTGGCCCCGAGCCTCAGGACGAAGACCAGAAGGACGCACTTCCGAGTGGAGGAGCTGGTTCATCTCTGAGCCAGGGTGACCCTGACGCAGCCATCTGGTTGGGAGATTCGCTGGGATCGATGACTCAGAAAAGCGACCTGTCCTCCTCATCTGGGTCCCTGAGCTTGTCTCACGGCTCCAGCTCTCTAGAGCACAGATCAGAGGACAGCACCATCTATGATCTCCTGAAGGATCCTGTCTCGCTGAGAAGCAAAGCACGCCGGGCCAAGAAAGCCAAGGCCAGCTCGGCGCTGGTGGTCTGTGGAGGGCAGGGCCACCGCCGGGTGCACAGGAAGGCCCGGCAGCCCCACCAGGAAGAGCTGGCGCCGACCGTCATGGTCTGGCAGATCCCTCTGCTGAATATATAAGCAGGACGGCCGCCTTCTGCTGTCAGAATTTGCAATCAAGGGTGACTTCTCAGCTAATCCTACAGCCTGAGTGGTTAAGCTGTGTCTACACTGGTTGGGAATAAATTAAAAACAGTATTTGGGGGAGAAACGTGCAATAGCGTAATGGTGGTGTCCCTGCCAATTCCTTCCTTCTCTTCTGTACAGCAGAAGTAATTACAAGCACTTCTCACGAAGGCAGAAGACTGATGCAATTTTCGAGTAATTGAGTGCAGTTCTGGGAAAATACCACATTCTTTTTGACTGCTGTAGTCCATATATGAATACTAAATGTTAAACTTCATCAGCGTCAGACCTATTGTATCATATTAGAGAATTTGCAGACTAAGAATTTATGAGAAAATATATGTATTCAGTAGTGCAGGCATTTATTAACAATTCTTAAAAGTTTTACCTGATTCAGATTCACGACTTTTATTTATATTCTATATTTTTGAATTTCAGAGTAAAATTTGTTAACAATTTTAAAAGCCAGGTAACACCTACCAGTCCAGTTAGCATGATTTGCTTTCAGAAGTGAGCTGGGTTTTCCAAAGTGGTATAATGTGTGTACTGTATATTTTAACAAAGTAATATTTTTGTATTGCATTTTTCTATTAAAAAATTAACAGTTAATGTTTCAGTCAATGTATTATCTGTAGCATTTCACAAATAATGTTTGCTTTGAACCAAAATGCTCAGTGCCTATCAACATTTGGACTCAAGCATCAACACCAAATTATTCCTCCCTTCTCGTATAAATAGAGTGACTATCCACAGGAGAAAAGTGTGTGCTTTAGTATTAGAGGAGATAGGCAGAGAAGTCTTGCTTAGTTCCTTCGTGCAGCTTCTTGCCCCTGTTGACGTGGAATGCTGTGTCTGCTTTAGCACGCACGCTCCGAATGACTCCTGGTGCTAGGCCATGCTGGCTGCTGTCACTGAGCGGGACTCAGGCCAAGAGGCGTGACCTCGGGCCAGCCTGTCTGTTGTGCAGACGCCTCCTCTGCAGAACGCATCAGTTTCTATTCTGCAGTTGCAGAGCCAGCCCCGCGTGAGAACGTGCATAATGAGTGCACACCATCATGTCAAGGTGCATACTTAGTGAGCGCCATCCTGCTGAACGTGTATTTCAGTGTTTCACTTACTGGACGGATAACAAGAAAAAAATCCTAACACAGGCAGTCACCAGAAATAAATGTCTCAGCACTTTACAGATGACTAAAAATGTTAATTTTATGACTTAGCCAAATATGTTCTAGGTTGCATATATCCCCCATGTGAAAGTGATTTCTTCCCAAGCTTCTCAAACTGTTAGCTGCTGTCTGACTTCATCAATAAAGTATTTTTATTTT</NUCLEOTIDE_ORIGINAL>
    </SEQUENCE>
    <PREDICTED-ORF>
      <CODING-POTENTIAL>Protein coding</CODING-POTENTIAL>
      <CDS_SOURCE_START>1</CDS_SOURCE_START>
      <CDS_SOURCE_END>5589</CDS_SOURCE_END>
      <CDS_START>185</CDS_START>
      <CDS_END>4219</CDS_END>
      <LENGTH-OF-CDS>1344</LENGTH-OF-CDS>
      <ORIENTATION>forward</ORIENTATION>
      <FRAME>+2</FRAME>
      <FEATURE>Complete CDS</FEATURE>
      <CAI>0.769</CAI>
    </PREDICTED-ORF>
    <FUNCTION>
      <DEFINITION>
        <DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>NP_055444</DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>
        <DATA-SOURCE_IDENTITY>100.0</DATA-SOURCE_IDENTITY>
        <DATA-SOURCE_COVERAGE>100.0</DATA-SOURCE_COVERAGE>
        <DATA-SOURCE_HOMOLOGOUS_SPECIES>Homo sapiens</DATA-SOURCE_HOMOLOGOUS_SPECIES>
        <DATA-SOURCE_CURATION-STATUS>Human curated</DATA-SOURCE_CURATION-STATUS>
        <DATA-SOURCE_DEFINITION>Rho guanine nucleotide exchange factor 10.</DATA-SOURCE_DEFINITION>
        <DATA-SOURCE_SIMILARITY-CATEGORY>Identical to known human protein(Category I).</DATA-SOURCE_SIMILARITY-CATEGORY>
        <EXP-EVIDENCE>Protein evidence</EXP-EVIDENCE>
        <EXP-CODE>1</EXP-CODE>
        <GENENAME-SYMBOL_DDBJ-EMBL-GenBank>KIAA0294</GENENAME-SYMBOL_DDBJ-EMBL-GenBank>
        <GENE-FAMILY_NAME>DH (IPR000219).</GENE-FAMILY_NAME>
        <GENE-FAMILY_HIF-ID>HIF0003409</GENE-FAMILY_HIF-ID>
        <GENE-FAMILY-EVIDENCE-MOTIF>IPR000219</GENE-FAMILY-EVIDENCE-MOTIF>
      </DEFINITION>
      <GENE-ONTOLOGY>
        <DOMAIN_DB-REFERENCE_INTERPRO>IPR000219</DOMAIN_DB-REFERENCE_INTERPRO>
        <DOMAIN_NAME>DH</DOMAIN_NAME>
        <DOMAIN_TYPE>Domain</DOMAIN_TYPE>
        <DOMAIN>
          <DOMAIN_MOTIF_START>1346</DOMAIN_MOTIF_START>
          <DOMAIN_MOTIF_END>1942</DOMAIN_MOTIF_END>
          <DOMAIN_MOTIF_START>1370</DOMAIN_MOTIF_START>
          <DOMAIN_MOTIF_END>1933</DOMAIN_MOTIF_END>
          <DOMAIN_MOTIF_START>1382</DOMAIN_MOTIF_START>
          <DOMAIN_MOTIF_END>1930</DOMAIN_MOTIF_END>
        <DOMAIN_MOTIF>
          <GO_ORGANIZING-PLINCIPLE>Molecular function</GO_ORGANIZING-PLINCIPLE>
          <GO_DB-REFERENCE_GO>0005089</GO_DB-REFERENCE_GO>
          <GO_TERM>Rho guanyl-nucleotide exchange factor activity</GO_TERM>
        </DOMAIN_MOTIF>
        <DOMAIN_MOTIF>
          <GO_ORGANIZING-PLINCIPLE>Cellular component</GO_ORGANIZING-PLINCIPLE>
          <GO_DB-REFERENCE_GO>0005622</GO_DB-REFERENCE_GO>
          <GO_TERM>intracellular</GO_TERM>
        </DOMAIN_MOTIF>
        <DOMAIN_MOTIF>
          <GO_ORGANIZING-PLINCIPLE>Biological process</GO_ORGANIZING-PLINCIPLE>
          <GO_DB-REFERENCE_GO>0035023</GO_DB-REFERENCE_GO>
          <GO_TERM>regulation of Rho protein signal transduction</GO_TERM>
        </DOMAIN_MOTIF>
        </DOMAIN>
        <DOMAIN_DB-REFERENCE_INTERPRO>IPR011046</DOMAIN_DB-REFERENCE_INTERPRO>
        <DOMAIN_NAME>WD40-like</DOMAIN_NAME>
        <DOMAIN_TYPE>Domain</DOMAIN_TYPE>
        <DOMAIN>
          <DOMAIN_MOTIF_START>2987</DOMAIN_MOTIF_START>
          <DOMAIN_MOTIF_END>3646</DOMAIN_MOTIF_END>
        </DOMAIN>
      </GENE-ONTOLOGY>
      <CELLULAR-LOCATION>
        <CELLULAR-LOCATION_DATE-LAST-UPDATE>26-Dec-2007</CELLULAR-LOCATION_DATE-LAST-UPDATE>
        <CELLULAR-LOCATION_DATE-LAST-MODIFIED>26-Dec-2007</CELLULAR-LOCATION_DATE-LAST-MODIFIED>
        <CELLULAR-LOCATION_SUBCELLULAR-RELEASE>5.0</CELLULAR-LOCATION_SUBCELLULAR-RELEASE>
        <LOCATION_WPSORT>plasma membrane</LOCATION_WPSORT>
        <LOCATION_WPSORT>endoplasmic</LOCATION_WPSORT>
        <LOCATION_WPSORT>cytosol</LOCATION_WPSORT>
        <LOCATION_WPSORT>nuclear</LOCATION_WPSORT>
        <TARGET-P>Other</TARGET-P>
        <SOSUI>membrane protein</SOSUI>
        <TMHMM>soluble protein</TMHMM>
        <PTS1>
          <LOCATION>Not targeted</LOCATION>
        </PTS1>
      </CELLULAR-LOCATION>
    </FUNCTION>
    <PROTEIN-STRUCTURE>
      <PROTEIN-STRUCTURE_DATE-LAST-UPDATE>26-Dec-2007</PROTEIN-STRUCTURE_DATE-LAST-UPDATE>
      <PROTEIN-STRUCTURE_DATE-LAST-MODIFIED>30-Mar-2007</PROTEIN-STRUCTURE_DATE-LAST-MODIFIED>
      <PROTEIN-STRUCTURE_3D-STRUCTURE-RELEASE>5.0</PROTEIN-STRUCTURE_3D-STRUCTURE-RELEASE>
      <SECONDARY-TERTIARY-STRUCTURE>
        <STRUCTURE_START>388</STRUCTURE_START>
        <STRUCTURE_END>598</STRUCTURE_END>
        <STRUCTURE_DB-REFERENCE_PDB>1by1A</STRUCTURE_DB-REFERENCE_PDB>
        <STRUCTURE_EVALUE>9e-27</STRUCTURE_EVALUE>
        <STRUCTURE_IDENTITY>18.6</STRUCTURE_IDENTITY>
        <STRUCTURE_COVERAGE>204/209</STRUCTURE_COVERAGE>
        <STRUCTURE_DOMAIN_DB-REFERENCE_SCOP>a.87.1.1</STRUCTURE_DOMAIN_DB-REFERENCE_SCOP>
        <STRUCTURE_DOMAIN_ANOMALOUS-STRUCTURE>YES</STRUCTURE_DOMAIN_ANOMALOUS-STRUCTURE>
      </SECONDARY-TERTIARY-STRUCTURE>
    </PROTEIN-STRUCTURE>
    <SEQUENCE_TRANSLATION>MDQREPLPPAPAENEMKYDTNNNEEEEGEQFDFDSGDEIPEADRQAPSAPETGGAGASEAPAPTGGEDGAGAETTPVAEPTKLVLPMKVNPYSVIDITPFQEDQPPTPVPSAEEENVGLHVPCGYLVPVPCGYAVPSNLPLLLPAYSSPVIICATSLDEEETPEVTEDRQPNSLSSEEPPTSEDQVGREDSALARWAADPANTAWMENPEEAIYDDVPRENSDSEPDEMIYDDVENGDEGGNSSLEYGWSSSEFESYEEQSDSECKNGIPRSFLRSNHKKQLSHDLTRLKEHYEKKMRDLMASTVGVVEIQQLRQKHELKMQKLVKAAKDGTKDGLERTRAAVKRGRSFIRTKSLIAQDHRSSLEEEQNLFIDVDCKHPEAILTPMPEGLSQQQVVRRYILGSVVDSEKNYVDALKRILEQYEKPLSEMEPKVLSERKLKTVFYRVKEILQCHSLFQIALASRVSEWDSVEMIGDVFVASFSKSMVLDAYSEYVNNFSTAVAVLKKTCATKPAFLEFLKQEQEASPDRTTLYSLMMKPIQRFPQFILLLQDMLKNTSKGHPDRLPLQMALTELETLAEKLNERKRDADQRCEVKQIAKAINERYLNKLLSSGSRYLIRSDDMIETVYNDRGEIVKTKERRVFMLNDVLMCATVSSRPSHDSRVMSSQRYLLKWSVPLGHVDAIEYGSSAGTGEHSRHLAVHPPESLAVVANAKPNKVYMGPGQLYQDLQNLLHDLNVIGQITQLIGNLKGNYQNLNQSVAHDWTSGLQRLILKKEDEIRAADCCRIQLQLPGKQDKSGRPTFFTAVFNTFTPAIKESWVNSLQMAKLALEEENHMGWFCVEDDGNHIKKEKHPLLVGHMPVMVAKQQEFKIECAAYNPEPYLNNESQPDSFSTAHGFLWIGSCTHQMGQIAIVSFQNSTPKVIECFNVESRILCMLYVPVEEKRREPGAPPDPETPAVRASDVPTICVGTEEGSISIYKSSQGSKKVRLQHFFTPEKSTVMSLACTSQSLYAGLVNGAVASYARAPDGSWDSEPQKVIKLGVLPVRSLLMMEDTLWAASGGQVFIISVETHAVEGQLEAHQEEGMVISHMAVSGVGIWIAFTSGSTLRLFHTETLKHLQDINIATPVHNMLPGHQRLSVTSLLVCHGLLMVGTSLGVLVALPVPRLQGIPKVTGRGMVSYHAHNSPVKFIVLATALHEKDKDKSRDSLAPGPEPQDEDQKDALPSGGAGSSLSQGDPDAAIWLGDSLGSMTQKSDLSSSSGSLSLSHGSSSLEHRSEDSTIYDLLKDPVSLRSKARRAKKAKASSALVVCGGQGHRRVHRKARQPHQEELAPTVMVWQIPLLNI*</SEQUENCE_TRANSLATION>
    <EXPRESSION>
      <EXPRESSION_DATE-LAST-UPDATE>26-Dec-2007</EXPRESSION_DATE-LAST-UPDATE>
      <EXPRESSION_DATE-LAST-MODIFIED>26-Dec-2007</EXPRESSION_DATE-LAST-MODIFIED>
      <PROBE-MAPPING>
        <PLATFORM>
          <PLATFORM-TYPE>AceGene</PLATFORM-TYPE>
          <PROBE>
            <PROBE-TYPE>AceGene</PROBE-TYPE>
            <PROBE-ID>AGhsA061219</PROBE-ID>
          </PROBE>
        </PLATFORM>
        <PLATFORM>
          <PLATFORM-TYPE>Affymetrix GeneChip</PLATFORM-TYPE>
          <PROBE>
            <PROBE-TYPE>HG-Focus</PROBE-TYPE>
            <PROBE-ID>216620_s_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HG-U133</PROBE-TYPE>
            <PROBE-ID>216620_s_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HG-U133A</PROBE-TYPE>
            <PROBE-ID>216620_s_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HG-U133A_2</PROBE-TYPE>
            <PROBE-ID>216620_s_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HG-U133_Plus_2</PROBE-TYPE>
            <PROBE-ID>216620_s_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HG-U95</PROBE-TYPE>
            <PROBE-ID>34180_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HG-U95A</PROBE-TYPE>
            <PROBE-ID>34180_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HG_U95Av2</PROBE-TYPE>
            <PROBE-ID>34180_at</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>HuEx-1_0</PROBE-TYPE>
            <PROBE-ID>3082875</PROBE-ID>
            <PROBE-ID>3082877</PROBE-ID>
            <PROBE-ID>3082878</PROBE-ID>
            <PROBE-ID>3082882</PROBE-ID>
            <PROBE-ID>3082883</PROBE-ID>
            <PROBE-ID>3082886</PROBE-ID>
            <PROBE-ID>3082887</PROBE-ID>
            <PROBE-ID>3082888</PROBE-ID>
            <PROBE-ID>3082892</PROBE-ID>
            <PROBE-ID>3082899</PROBE-ID>
            <PROBE-ID>3082900</PROBE-ID>
            <PROBE-ID>3082901</PROBE-ID>
            <PROBE-ID>3082902</PROBE-ID>
            <PROBE-ID>3082903</PROBE-ID>
            <PROBE-ID>3082904</PROBE-ID>
            <PROBE-ID>3082908</PROBE-ID>
            <PROBE-ID>3082909</PROBE-ID>
            <PROBE-ID>3082910</PROBE-ID>
            <PROBE-ID>3082917</PROBE-ID>
            <PROBE-ID>3082919</PROBE-ID>
            <PROBE-ID>3082926</PROBE-ID>
            <PROBE-ID>3082927</PROBE-ID>
            <PROBE-ID>3082928</PROBE-ID>
            <PROBE-ID>3082929</PROBE-ID>
            <PROBE-ID>3082930</PROBE-ID>
            <PROBE-ID>3082932</PROBE-ID>
            <PROBE-ID>3082936</PROBE-ID>
            <PROBE-ID>3082937</PROBE-ID>
            <PROBE-ID>3082940</PROBE-ID>
            <PROBE-ID>3082944</PROBE-ID>
            <PROBE-ID>3082948</PROBE-ID>
            <PROBE-ID>3082950</PROBE-ID>
            <PROBE-ID>3082951</PROBE-ID>
            <PROBE-ID>3121542</PROBE-ID>
            <PROBE-ID>3121578</PROBE-ID>
            <PROBE-ID>3121579</PROBE-ID>
          </PROBE>
        </PLATFORM>
        <PLATFORM>
          <PLATFORM-TYPE>Agilent probe set</PLATFORM-TYPE>
          <PROBE>
            <PROBE-TYPE>Human 1A Oligo Microarray:PGID215</PROBE-TYPE>
            <PROBE-ID>A_23_P216282</PROBE-ID>
          </PROBE>
          <PROBE>
            <PROBE-TYPE>Whole Human Genome Oligo Microarray:PGID247</PROBE-TYPE>
            <PROBE-ID>A_23_P216282</PROBE-ID>
            <PROBE-ID>A_24_P283535</PROBE-ID>
          </PROBE>
        </PLATFORM>
      </PROBE-MAPPING>
    </EXPRESSION>
  </cDNAXML>
</H-Inv>

In bioruby:

simple access

irb(main):051:0> Bio::Hinv.hit_xml("HIT000000001")
=> "<?xml version="1.0" standalone="yes" ?> ...

and (incomplete) full access

irb(main):005:0> serv = Bio::Hinv::HitXML.new
irb(main):006:0> serv.query("hit" =>"HIT000000001")
irb(main):007:0> serv.result
=> "Rho guanine nucleotide exchange factor 10."
irb(main):071:0> a.instance_eval { @xml.elements.each("//MOL-TYPE") {|x| p x.text } }
"mRNA"
=> [<MOL-TYPE> ... </>]

hix2hit - HIT ID of HIT ID

URI:

Output:

<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
<H-INVITATIONAL-ID>HIT000012846</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022124</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000007722</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000281202</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000293297</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000283989</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000299690</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000284643</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000280349</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000297167</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000274447</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000301319</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000293727</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000261011_01</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000339817</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000301513</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000088658_01</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000393264</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000262478</H-INVITATIONAL-ID>
</H-Inv>

In bioruby:

irb(main):007:0> Bio::Hinv.hix2hit("HIX0000001")
=> ["HIT000022181"]
|ruby|<

** hix_cnt - total number of HIX ID
URI:
- http://jbirc.jbic.or.jp/hinv/hws/hix_cnt.php

Output:
>|xml|
<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
        <LOCUS_CNT>36073</LOCUS_CNT>
</H-Inv>

In bioruby:

irb(main):078:0> Bio::Hinv.hix_cnt
=> 36073

hix_represent - representative HIT ID of HIX ID

URI:

Output:

<?xml version='1.0' encoding='UTF-8'?>
<H-Inv>
        <LOCUS>
                <CLUSTER-ID>HIX0000001</CLUSTER-ID>
                <REP-H-INVITATIONAL-ID>HIT000022181</REP-H-INVITATIONAL-ID>
                <REP-ACCESSION-NO>AK097327</REP-ACCESSION-NO>
        </LOCUS>
</H-Inv>

In bioruby:

irb(main):079:0> Bio::Hinv.hix_represent("HIX0000001")
=> "HIT000022181"
irb(main):081:0> serv=Bio::Hinv::HixRepresent.new
irb(main):082:0> serv.query("hix"=>"HIX0000001")
irb(main):085:0> serv.rep_accession_no
=> "AK097327"
irb(main):086:0> serv.rep_h_invitational_id
=> "HIT000022181"

hix_xml - HIX XML file of HIX ID

URI:

Output:



			

In bioruby:



			

id_search - HIT ID of any ID

URI:


Output:

<?xml version='1.0' encoding='UTF-8'?>
<HINVDB_SEARCH>
<QUERY>HIT00002218*</QUERY>
<ID_TYPE>H-INVITATIONAL-ID</ID_TYPE>
<SIZE>8</SIZE>
<START>1</START>
<END>8</END>
<H-INVITATIONAL-ID>HIT000022181</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022184</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022189</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022180</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022185</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022183</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022188</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022186</H-INVITATIONAL-ID>
</HINVDB_SEARCH>||<

In bioruby:
>|ruby|
irb(main):088:0> Bio::Hinv.id_search("HIT00002218*")
=> ["HIT000022181", "HIT000022184", "HIT000022189", "HIT000022180", "HIT000022185", "HIT000022183", "HIT000022188", "HIT000022186"]
irb(main):090:0> serv = Bio::Hinv::IdSearch.new
irb(main):093:0> serv.query("query" => "HIT00002218*", "start" => "1", "end" => "100")

keyword_search - HIT ID of any ID

URI:


Output:

<?xml version='1.0' encoding='UTF-8'?>
<HINVDB_SEARCH>
<QUERY>HIT00002218*</QUERY>
<SIZE>8</SIZE>
<START>1</START>
<END>8</END>
<H-INVITATIONAL-ID>HIT000022180</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022181</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022183</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022184</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022185</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022186</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022188</H-INVITATIONAL-ID>
<H-INVITATIONAL-ID>HIT000022189</H-INVITATIONAL-ID>
</HINVDB_SEARCH>

In bioruby:

irb(main):089:0> Bio::Hinv.keyword_search("HIT00002218*")
=> ["HIT000022180", "HIT000022181", "HIT000022183", "HIT000022184", "HIT000022185", "HIT000022186", "HIT000022188", "HIT000022189"]
irb(main):090:0> serv = Bio::Hinv::KeywordSearch.new
irb(main):093:0> serv.query("query" => "HIT00002218*", "start" => "1", "end" => "100")

Summary

  1. Classes for H-InvDB REST web service are available on BioRuby CVS HEAD.
  2. Access methods for some complicated outputs are no implemented.
  3. URI design of the H-InvDB REST web service is not good. For example, acc2hit api contains redundunt "acc" term twice (http://jbirc.jbic.or.jp/hinv/hws/acc2hit.php?acc=BC053657).
トラックバック - http://bioruby.g.hatena.ne.jp/nakao_mitsuteru/20080110

2007-12-30

BioRuby 1.2.1 released

|  BioRuby 1.2.1 released - "aac".translate #=> "N" を含むブックマーク はてなブックマーク -  BioRuby 1.2.1 released - "aac".translate #=> "N"  BioRuby 1.2.1 released - "aac".translate #=> "N" のブックマークコメント

Katayama-san announced the BioRuby 1.2.1 release today.

Hi all,

I just released the BioRuby 1.2.1 including fix for BLAST 2.2.17 output.

Note that this version is not yet Ruby 1.9 compliant.

http://bioruby.org/archive/bioruby-1.2.1.tar.gz

http://rubyforge.org/projects/bioruby/

You can see changes at

http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/ChangeLog?rev=1.79&cvsroot=bioruby

P.S.

Unfortunately, I removed the RAA entry for BioRuby by mistake (I need to sleep now :).

I immediately re-added as a new project but our history was lost.

http://raa.ruby-lang.org/project/bioruby/

I took a screenshot of the old admin screen for record.

http://bioruby.org/tmp/bioruby-deleted-raa.png

Happy holidays!

Regards,

Toshiaki Katayama

http://lists.open-bio.org/pipermail/bioruby/2007-December/000519.html
トラックバック - http://bioruby.g.hatena.ne.jp/nakao_mitsuteru/20071230

2007-12-25

bioruby CVS HEAD on ruby 1.9.0

|  bioruby CVS HEAD on ruby 1.9.0  - "aac".translate #=> "N" を含むブックマーク はてなブックマーク -  bioruby CVS HEAD on ruby 1.9.0  - "aac".translate #=> "N"  bioruby CVS HEAD on ruby 1.9.0  - "aac".translate #=> "N" のブックマークコメント

Matz released Ruby 1.9.0 today (tmorrow ?). So I checked the bioruby test suits.

There are known issues (related with bioruby),

  1. soap4r,
  2. gem and
  3. some methods removed (String#each, String#collect.

SyntaxError

First off, I got a SyntaxError to run the tests.

$ /usr/local/bin/ruby install.rb test
install.rb: entering test phase...
Running all tests in test...
/usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:90:in `require': /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_alignment.rb:430: syntax error, unexpected ']' (SyntaxError)
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:90:in `collect_file'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:73:in `block in recursive_collect'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:58:in `each'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:58:in `recursive_collect'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:63:in `block in recursive_collect'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:58:in `each'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:58:in `recursive_collect'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:63:in `block in recursive_collect'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:58:in `each'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:58:in `recursive_collect'
        from /usr/local/lib/ruby/1.9.0/test/unit/collector/dir.rb:29:in `collect'
        from /usr/local/lib/ruby/1.9.0/test/unit/autorunner.rb:68:in `block (1 levels) in <class:AutoRunner>'
        from /usr/local/lib/ruby/1.9.0/test/unit/autorunner.rb:213:in `[]'
        from /usr/local/lib/ruby/1.9.0/test/unit/autorunner.rb:213:in `run'
        from install.rb:671:in `exec_test'
        from install.rb:927:in `try'
        from install.rb:920:in `exectask'
        from install.rb:906:in `invoke'
        from install.rb:874:in `invoke'
        from install.rb:1108:in `<main>'

To solve it.

$ diff -u test/unit/bio/test_alignment.rb.\~1.11.\~ test/unit/bio/test_alignment.rb                                      07-12-26
--- test/unit/bio/test_alignment.rb.~1.11.~     2007-04-07 01:55:16.000000000 +0900
+++ test/unit/bio/test_alignment.rb     2007-12-26 01:29:27.000000000 +0900
@@ -426,7 +426,7 @@
         Sequence::AA.new('MNSA'),
         Sequence::AA.new('MHTL'),
         Sequence::AA.new('MQNV'),
-        Sequence::AA.new('MKKW'),
+        Sequence::AA.new('MKKW')
       ]
       assert_equal('*:. ', a.match_line)
       assert_equal('*:. ', a.match_line(:type => :aa))

1322 tests, 2384 assertions, 67 failures, 167 errors

I got so many errors from the bioruby test suits :-(

Just I show the terminal message.

$ /usr/local/bin/ruby install.rb test
install.rb: entering test phase...
Running all tests in test...
Loaded suite test
Started
..........EEEE.....................................................................E...........................................................................................................E...............E...........................F.FFFF..FE.............................................................................................................E..........................F...........EEFFFFF.FFFEEEEEEEEE........................................................................................EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE..................................................EEE.......................EEEEEEEEE.EEEEE.............................................................................................................................................FFFF..............................E..........................................FFFFFFFFFFFFFF...............EEE.E....................................F.FF.FFFF......F.....................F..E......FFFFF..............E....EEEEEEEEEEEEEEEEEEEEEEEEEE...F..........F.......E...EE....EE...EEF............................................FF.......................................................................................EEFF.FF..FF......F...FF.....F...FF....................FF.F.........................
Finished in 40.870631 seconds.

  1) Error:
test_log(Bio::FuncTestSOAPWSDL):
NameError: uninitialized constant Bio::SOAPWSDL::SOAP
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:63:in `create_driver'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:57:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `setup'

  2) Error:
test_set_log(Bio::FuncTestSOAPWSDL):
NameError: uninitialized constant Bio::SOAPWSDL::SOAP
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:63:in `create_driver'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:57:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `setup'

  3) Error:
test_set_wsdl(Bio::FuncTestSOAPWSDL):
NameError: uninitialized constant Bio::SOAPWSDL::SOAP
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:63:in `create_driver'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:57:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `setup'

  4) Error:
test_wsdl(Bio::FuncTestSOAPWSDL):
NameError: uninitialized constant Bio::SOAPWSDL::SOAP
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:63:in `create_driver'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/io/soapwsdl.rb:57:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/functional/bio/io/test_soapwsdl.rb:25:in `setup'

  5) Error:
test_each_window(Bio::TestAlignmentEnumerableExtension):
NoMethodError: undefined method `+' for nil:NilClass
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/alignment.rb:488:in `each_window'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_alignment.rb:329:in `test_each_window'

  6) Error:
test_cliquishness(Bio::TestMyGraph):
ArgumentError: wrong number of arguments (0 for 1)
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:25:in `sum'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:65:in `cliquishness'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:82:in `test_cliquishness'

  7) Error:
test_format_bibitem(Bio::TestReference):
NoMethodError: undefined method `collect' for #<String:0x243ab78>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/reference.rb:263:in `bibitem'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/reference.rb:176:in `format'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_reference.rb:100:in `test_format_bibitem'

  8) Failure:
test_depth_first_search(Bio::TestSampleGraph) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:291]:
timestamps wrong.
<{"v"=>[1, 6],
 "w"=>[2, 5],
 "x"=>[7, 10],
 "y"=>[11, 16],
 "z"=>[8, 9],
 "q"=>[12, 15],
 "r"=>[17, 20],
 "s"=>[3, 4],
 "t"=>[13, 14],
 "u"=>[18, 19]}> expected but was
<{"q"=>[1, 16],
 "s"=>[2, 7],
 "v"=>[3, 6],
 "w"=>[4, 5],
 "t"=>[8, 15],
 "x"=>[9, 12],
 "z"=>[10, 11],
 "y"=>[13, 14],
 "r"=>[17, 20],
 "u"=>[18, 19]}>.

  9) Failure:
test_dump_list(Bio::TestSampleGraph) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:184]:
<"v => w (1)\nw => s (1)\nx => z (1)\ny => q (1)\nz => x (1)\nq => w (1), s (1), t (1)\nr => y (1), u (1)\ns => v (1)\nt => x (1), y (1)\nu => y (1)\n"> expected but was
<"q => s (1), t (1), w (1)\ns => v (1)\nt => x (1), y (1)\nw => s (1)\nr => u (1), y (1)\nu => y (1)\ny => q (1)\nv => w (1)\nx => z (1)\nz => x (1)\n">.

 10) Failure:
test_dump_matrix(Bio::TestSampleGraph) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:170]:
<"[# v, w, x, y, z, q, r, s, t, u\n [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],\n [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],\n [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],\n [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],\n [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],\n [0, 1, 0, 0, 0, 0, 0, 1, 1, 0],\n [0, 0, 0, 1, 0, 0, 0, 0, 0, 1],\n [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],\n [0, 0, 0, 1, 0, 0, 0, 0, 0, 0]\n]"> expected but was
<"[# q, s, t, w, r, u, y, v, x, z\n [0, 1, 1, 1, 0, 0, 0, 0, 0, 0],\n [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],\n [0, 0, 0, 0, 0, 0, 1, 0, 1, 0],\n [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],\n [0, 0, 0, 0, 0, 1, 1, 0, 0, 0],\n [0, 0, 0, 0, 0, 0, 1, 0, 0, 0],\n [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n [0, 0, 0, 1, 0, 0, 0, 0, 0, 0],\n [0, 0, 0, 0, 0, 0, 0, 0, 0, 1],\n [0, 0, 0, 0, 0, 0, 0, 0, 1, 0]\n]">.

 11) Failure:
test_extract_subgraph_by_label(Bio::TestSampleGraph) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:195]:
<"v => w (1)\nw => s (1)\nq => w (1), s (1)\ns => v (1)\n"> expected but was
<"q => s (1), w (1)\ns => v (1)\nw => s (1)\nv => w (1)\n">.

 12) Failure:
test_extract_subgraph_by_list(Bio::TestSampleGraph) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:205]:
<"x => z (1)\ny => q (1)\nz => x (1)\nq => t (1)\nt => x (1), y (1)\n"> expected but was
<"q => t (1)\nt => x (1), y (1)\ny => q (1)\nx => z (1)\nz => x (1)\n">.

 13) Failure:
test_to_matrix(Bio::TestSampleGraph) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:153]:
matrix wrong.
<Matrix[[0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 1, 1, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 1], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0]]> expected but was
<Matrix[[0, 1, 1, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 1, 0], [0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 1, 1, 0, 0, 0], [0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1], [0, 0, 0, 0, 0, 0, 0, 0, 1, 0]]>.

 14) Error:
test_undirected_cliquishness(Bio::TestSampleGraph):
ArgumentError: wrong number of arguments (0 for 1)
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:25:in `sum'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:65:in `cliquishness'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/test_pathway.rb:230:in `test_undirected_cliquishness'

 15) Error:
test_blast_reports(Bio::TestBlast):
NoMethodError: undefined method `each' for #<String:0x2517d70>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/blast.rb:109:in `reports'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_blast.rb:125:in `test_blast_reports'

 16) Failure:
test_option(Bio::TestFasta) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_fasta.rb:99]:
<"[\"-M\"]"> expected but was
<"\\[-M\\]">.

 17) Error:
test_exec(Bio::TestPTS1):
NoMethodError: undefined method `each' for #<String:0x249ab68>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:85:in `test_exec'

 18) Error:
test_exec_with_faa(Bio::TestPTS1):
NoMethodError: undefined method `each' for #<String:0x2497490>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:90:in `test_exec_with_faa'

 19) Failure:
test_function_set(Bio::TestPTS1) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:61]:
<"GENERAL"> expected but was
<"[\"GENERAL\"]">.

 20) Failure:
test_function_set_number_1(Bio::TestPTS1) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:70]:
<"METAZOA-specific"> expected but was
<"[\"METAZOA-specific\"]">.

 21) Failure:
test_function_set_number_2(Bio::TestPTS1) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:75]:
<"FUNGI-specific"> expected but was
<"[\"FUNGI-specific\"]">.

 22) Failure:
test_function_set_number_3(Bio::TestPTS1) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:80]:
<"GENERAL"> expected but was
<"[\"GENERAL\"]">.

 23) Failure:
test_function_show(Bio::TestPTS1) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:65]:
<"METAZOA-specific"> expected but was
<"[\"METAZOA-specific\"]">.

 24) Failure:
test_fungi(Bio::TestPTS1New) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:37]:
<"FUNGI-specific"> expected but was
<"[\"FUNGI-specific\"]">.

 25) Failure:
test_general(Bio::TestPTS1New) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:42]:
<"GENERAL"> expected but was
<"[\"GENERAL\"]">.

 26) Failure:
test_metazoa(Bio::TestPTS1New) [/Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:32]:
<"METAZOA-specific"> expected but was
<"[\"METAZOA-specific\"]">.

 27) Error:
test_cterm(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x2466598>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 28) Error:
test_entry_id(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x2462c04>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 29) Error:
test_fp(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x245f48c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 30) Error:
test_output_size(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x245c4d0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 31) Error:
test_prediction(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x24592e4>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 32) Error:
test_profile(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x24543e8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 33) Error:
test_score(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x2450784>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 34) Error:
test_sppta(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x244c918>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 35) Error:
test_spptna(Bio::TestPTS1Report):
NoMethodError: undefined method `each' for #<String:0x244846c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:232:in `parse'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:222:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/pts1.rb:155:in `exec'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/test_pts1.rb:100:in `setup'

 36) Error:
test_date_run(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x25134b4>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 37) Error:
test_gccontent(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x2510674>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 38) Error:
test_genscan_version(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x250bc64>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 39) Error:
test_isochore(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x2508dfc>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 40) Error:
test_length(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x2505a58>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 41) Error:
test_matrix(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x2502100>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 42) Error:
test_predictions_size(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x24fe564>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 43) Error:
test_query_name(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x24f7390>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 44) Error:
test_time(Bio::TestGenscanReport):
NoMethodError: undefined method `each' for #<String:0x24f2f48>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:27:in `setup'

 45) Error:
test_acceptor_score(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24f0388>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 46) Error:
test_donor_score(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24e9114>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 47) Error:
test_exon_type(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24e5cf8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 48) Error:
test_exon_type_long(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24e25bc>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 49) Error:
test_first(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24ded18>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 50) Error:
test_initiation_score(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24db8c0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 51) Error:
test_last(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24d8a6c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 52) Error:
test_number(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24d595c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 53) Error:
test_p_value(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24d24dc>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 54) Error:
test_phase(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24cecb0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 55) Error:
test_range(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24cb59c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 56) Error:
test_score(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24c7f78>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 57) Error:
test_strand(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24c5214>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 58) Error:
test_t_score(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24c2550>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 59) Error:
test_termination_score(Bio::TestGenscanReportExon):
NoMethodError: undefined method `each' for #<String:0x24bf314>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:117:in `setup'

 60) Error:
test_aaseq(Bio::TestGenscanReportGene):
NoMethodError: undefined method `each' for #<String:0x24bc04c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `setup'

 61) Error:
test_naseq(Bio::TestGenscanReportGene):
NoMethodError: undefined method `each' for #<String:0x24b920c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `setup'

 62) Error:
test_number(Bio::TestGenscanReportGene):
NoMethodError: undefined method `each' for #<String:0x24b1b88>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `setup'

 63) Error:
test_polyA(Bio::TestGenscanReportGene):
NoMethodError: undefined method `each' for #<String:0x24ac818>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `setup'

 64) Error:
test_promoter(Bio::TestGenscanReportGene):
NoMethodError: undefined method `each' for #<String:0x24a9dd4>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/genscan/report.rb:78:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/genscan/test_report.rb:75:in `setup'

 65) Error:
test_reports_ary(Bio::TestHMMERReportClassMethods):
NoMethodError: undefined method `each' for #<String:0x24a9564>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:64:in `reports'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:45:in `test_reports_ary'

 66) Error:
test_accession(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x24a7d04>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 67) Error:
test_append_hsp(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x24a6a44>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 68) Error:
test_bit_score(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x24a5950>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 69) Error:
test_definition(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x24a4640>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 70) Error:
test_description(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x24a32b8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 71) Error:
test_each(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x24a1f58>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 72) Error:
test_each_hsp(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x24a0bd0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 73) Error:
test_entry_id(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x249fc44>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 74) Error:
test_evalue(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x249ece0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 75) Error:
test_hit(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x249db10>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 76) Error:
test_hit_id(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x249c92c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 77) Error:
test_hsps(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x249b888>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 78) Error:
test_num(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x249a7e4>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 79) Error:
test_score(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x249927c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 80) Error:
test_target_def(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x2497fd0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 81) Error:
test_target_id(Bio::TestHMMERReportHit):
NoMethodError: undefined method `each' for #<String:0x2496e00>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:130:in `setup'

 82) Error:
test_domain_top_hits(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x24959d8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 83) Error:
test_each(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x2494a4c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 84) Error:
test_each_hit(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x2493a98>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 85) Error:
test_histogram(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x2492a58>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 86) Error:
test_hits(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x2491608>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 87) Error:
test_hsps(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x2490578>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 88) Error:
test_parameter(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x248f600>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 89) Error:
test_program(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x248e548>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 90) Error:
test_query_info(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x248d10c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 91) Error:
test_statistical_detail(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x248bb68>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 92) Error:
test_total_seq_searched(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x248a948>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 93) Error:
test_whole_seq_top_hits(Bio::TestHMMERReportHmmpfam):
NoMethodError: undefined method `each' for #<String:0x24899d0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:62:in `setup'

 94) Error:
test_domain_top_hits(Bio::TestHMMERReportHmmsearch):
NoMethodError: undefined method `each' for #<String:0x2488a6c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `setup'

 95) Error:
test_histogram(Bio::TestHMMERReportHmmsearch):
NoMethodError: undefined method `each' for #<String:0x2487ae0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `setup'

 96) Error:
test_statistical_detail(Bio::TestHMMERReportHmmsearch):
NoMethodError: undefined method `each' for #<String:0x2486b2c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `setup'

 97) Error:
test_total_seq_searched(Bio::TestHMMERReportHmmsearch):
NoMethodError: undefined method `each' for #<String:0x2485bb4>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `setup'

 98) Error:
test_whole_seq_top_hit(Bio::TestHMMERReportHmmsearch):
NoMethodError: undefined method `each' for #<String:0x2484b88>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:305:in `setup'

 99) Error:
test_accession(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2483b84>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

100) Error:
test_bit_score(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2482bd0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

101) Error:
test_csline(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2481b90>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

102) Error:
test_domain(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2480ba0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

103) Error:
test_evalue(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x247fac0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

104) Error:
test_flatseq(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x247ea44>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

105) Error:
test_hmm_f(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x247da04>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

106) Error:
test_hmm_t(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x247c9ec>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

107) Error:
test_hmmseq(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x247a9d0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

108) Error:
test_hsp(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2476448>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

109) Error:
test_midline(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2473aa4>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

110) Error:
test_query_frame(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2470034>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

111) Error:
test_query_from(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x246edd8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

112) Error:
test_query_seq(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x246de4c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

113) Error:
test_query_to(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x246c8a8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

114) Error:
test_rfline(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x246b5e8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

115) Error:
test_score(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x246a710>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

116) Error:
test_seq_f(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x24692e8>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

117) Error:
test_seq_ft(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x24682d0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

118) Error:
test_seq_t(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x24673d0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

119) Error:
test_set_alignment(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x24664e4>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

120) Error:
test_targat_to(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x246484c>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

121) Error:
test_target_frame(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2463960>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

122) Error:
test_target_from(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x2462a74>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

123) Error:
test_target_seq(Bio::TestHMMERReportHsp):
NoMethodError: undefined method `each' for #<String:0x24612f0>
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:270:in `parse_header_data'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/lib/bio/appl/hmmer/report.rb:165:in `initialize'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `new'
    /Users/nakao/Documents/src/Bio/bioruby/current/HEAD/test/unit/bio/appl/hmmer/test_report.rb:201:in `setup'

124) Error:
test_alignment(Bio::TestAlignmentMultiFastaFormat):
ArgumentError: wrong number of arguments(2 for 1)
    /Users/nakao/D
		
トラックバック - http://bioruby.g.hatena.ne.jp/nakao_mitsuteru/20071225