[Bioperl-l] IMGT parsing

Brian Osborne brian_osborne at cognia.com
Fri Feb 18 07:37:11 EST 2005


Have you tested this change by reading through some large file of
EMBL-formatted sequences? The more you've tested this the happier I'd be to
change embl.pm for you.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Alex Brown
Sent: Friday, February 18, 2005 6:16 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] IMGT parsing


I had a small problem using BioSeqIO (in BioPerl 1.4) to parse the IMGT
flat file database - although the IMGT uses an EMBL-like format,
BioSeqIO was unable to extract display_id(), which is a bit of a
nuisance when converting between formats. This is due to a difference
between the ID line of the EMBL and the IMGT formats:

ID   TRBG361    standard; mRNA; PLN; 1859 BP.

ID   MMTCRGBV1 IMGT/LIGM annotation : by annotators; RNA; ROD; 290 BP.

The following modification to embl.pm seems to allowing correct parsing
of both formats :
change the lines:

    $line =~ /^ID\s+\S+/ || $self->throw("EMBL stream with no ID. Not
embl in my book");
      $line =~ /^ID\s+(\S+)\s+\S+\;\s+([^;]+)\;\s+(\S+)\;/;
      $name = $1;
      $mol = $2;
      $div = $3;
      if(! $name) {
          $name = "unknown id";

to :

    $line =~ /^ID\s+\S+/ || $self->throw("EMBL stream with no ID. Not
embl in my book");
      # this is the new line to replace the above, allowing IMGT records
to be read as well
      ($name, $mol, $div) = ($line =~
      if(! $name) {
          $name = "unknown id";

Hope this is useful.

Alex Brown.

PS. BACK-UP embl.pm before changing.

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