[Bioperl-guts-l] [Bug 2165] New: Bio::SeqIO does not write correct taxonomy data in SwissProt format

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Dec 14 03:55:34 EST 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=2165

           Summary: Bio::SeqIO does not write correct taxonomy data in
                    SwissProt format
           Product: Bioperl
           Version: unspecified
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::SeqIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: joerg.hau at rdls.nestle.com


Hi,

While trying to write a SwissProt DAT file, I found that the taxonomy/species
information is, uhm, "somewhat garbled". Example program:

#!/usr/local/bin/perl

use strict;
use warnings;

use Bio::Seq;
use Bio::SeqIO;
use Bio::Species;

my $seq_out = Bio::SeqIO->new('-fh' => \*STDOUT,
                            '-format' => "swiss");

my $seq = Bio::Seq->new(-seq => "SECRETSERVICE",
                            -accession_number => "007",
                            -display_id => "JAMES_BOND",
                            -desc => "It's secret, so no description here");

my $tax="Agentus secretus";
my $species = Bio::Species->new(-common_name => $tax);
$seq->species($species);    # This goes into the OS field
print "=> The common name is correctly stored in the species object: '" .
$seq->species->common_name . "'\n\n";

$seq_out->write_seq($seq);


If you run this, you get the following output:

---start output---
=> The common name is correctly stored in the species object: 'Agentus
secretus'

ID   JAMES_BOND     STANDARD;      PRT;   13 AA.
AC   007;
DE   It's secret, so no description here
OS     (Agentus secretus).
OC   .
KW
SQ   SEQUENCE    13 AA;  1541 MW;  8A48789883D405A1 CRC64;
     SECRETSERV ICE
//

---end output---

The lines that are wrong are OS and OC:

- The OS line should not have any parentheses around the common name, and the
text should start at column 6.
- The OC line should be absent, since no organism classification was given.

HTH, and happy bug squashing ;-)

- Joerg


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