BioPerl-Run

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lib/Bio/DB/SoapEUtilities.pm  view on Meta::CPAN

               -id => \@protein_ids )->run(-auto_adapt => 1);

 # get a Bio::DB::SoapEUtilities::Result object
 my $result = $fac->esearch(
               -db => 'gene',
               -term => 'sonic and human')->run;

 # get the raw XML message
 my $xml = $fac->efetch(
             -db => 'gene',
             -id => \@gids )->run( -raw_xml => 1 );

 # change parameters 
 my $new_result = $fac->efetch(
                   -db => 'gene',
                   -id => \@more_gids)->run;
 # reset parameters
 $fac->efetch->reset_parameters( -db => 'nucleotide',
                                 -id => $nucid );
 $result = $fac->efetch->run;
                
 # parsing and iterating the results

 $count = $result->count;
 @ids = $result->ids;
 

lib/Bio/Tools/Run/Phylo/Phyml.pm  view on Meta::CPAN

sub _write_phylip_align_file {
    my ( $self, $align ) = @_;

    my $tempfile = File::Spec->catfile( $self->tempdir, "aln$$.phylip" );
    $self->data_format('i');
    my $out = Bio::AlignIO->new(
        -file        => ">$tempfile",
        -format      => 'phylip',
        -interleaved => 1,
        -longid      => 1
    );
    $out->write_aln($align);
    $out->close();
    $out = undef;
    return $tempfile;
}

1;

t/data/gb_result.xml  view on Meta::CPAN

          <GBQualifier_name>db_xref</GBQualifier_name>
          <GBQualifier_value>PDB:1W30</GBQualifier_value>
        </GBQualifier>
        <GBQualifier>
          <GBQualifier_name>db_xref</GBQualifier_name>
          <GBQualifier_value>UniProtKB/Swiss-Prot:P65941</GBQualifier_value>
        </GBQualifier>
      </GBFeature_quals>
    </GBFeature>
  </GBSeq_feature-table>
  <GBSeq_sequence>mgaagdaaigresrelmsaadvgrtisriahqiiektalddpvgpdaprvvllgiptrgvtlanrlagniteysgihvghgalditlyrddlmikpprplastsipaggiddalvilvddvlysgrsvrsaldalrdvgrpravqlavlvdrghrelplradyvgknvptsrsesvhvrlrehdgrdgvvisr</GBSeq_sequence>
</GBSeq>

<GBSeq>
  <GBSeq_locus>EAS10332</GBSeq_locus>
  <GBSeq_length>193</GBSeq_length>
  <GBSeq_moltype>AA</GBSeq_moltype>
  <GBSeq_topology>linear</GBSeq_topology>
  <GBSeq_division>BCT</GBSeq_division>
  <GBSeq_update-date>09-APR-2007</GBSeq_update-date>
  <GBSeq_create-date>09-MAR-2006</GBSeq_create-date>

t/data/gb_result.xml  view on Meta::CPAN

          <GBQualifier_name>transl_table</GBQualifier_name>
          <GBQualifier_value>11</GBQualifier_value>
        </GBQualifier>
        <GBQualifier>
          <GBQualifier_name>db_xref</GBQualifier_name>
          <GBQualifier_value>InterPro:IPR000836</GBQualifier_value>
        </GBQualifier>
      </GBFeature_quals>
    </GBFeature>
  </GBSeq_feature-table>
  <GBSeq_sequence>mgapdqsgsdrelmsaadvsrtiariahqiiektaldgpdgprvillgiptrgvtlasrlatniaefsgvqvahgaldttlyrddlmtkppralaetsipaggidgalvilvddvlytgrsvrsaldalrdlgrpkavqlavlvdrghrelpiradyvgknvptsrsenvkvrltendgvdiiaiapyggppr</GBSeq_sequence>
</GBSeq>
</GBSet>

</eFetchResult>
</SOAP-ENV:Body>
</SOAP-ENV:Envelope>

t/data/taxdump/names.dmp  view on Meta::CPAN

9596	|	Pan	|		|	scientific name	|
9596	|	chimpanzees	|		|	genbank common name	|
9598	|	Chimpansee troglodytes	|		|	misspelling	|
9598	|	Pan troglodytes	|		|	scientific name	|
9598	|	chimpanzee	|		|	genbank common name	|
9599	|	Pongo	|		|	scientific name	|
9600	|	Pongo pygmaeus	|		|	scientific name	|
9600	|	orang-utan	|		|	common name	|
9600	|	orangutan	|		|	genbank common name	|
9604	|	Hominidae	|		|	scientific name	|
9604	|	Pongidae	|		|	synonym	|
9604	|	great apes	|		|	common name	|
9605	|	Homo	|		|	scientific name	|
9606	|	Homo sapiens	|		|	scientific name	|
9606	|	human	|		|	genbank common name	|
9606	|	man	|		|	common name	|
29089	|	Hylobates concolor	|		|	synonym	|
29089	|	Nomascus concolor	|		|	scientific name	|
29089	|	crested gibbon	|		|	genbank common name	|
32523	|	Tetrapoda	|		|	scientific name	|
32523	|	tetrapods	|		|	genbank common name	|