[Bioperl-l] parsing SwissProt records -- need help
Anand Venkatraman
bioperlanand at yahoo.com
Thu Oct 14 19:13:08 EDT 2004
HI,
I am new to Bioperl and I am using it to parse data
from SwissProt Records.
I am trying to get all the accession numbers from the
SwissProt file. I am facing problems when I have more
than 1 accession number in 1 line - like for example
-------------------------
AC P15456; Q9SAW0;
-------------------------
Sometimes they might go on for two lines as seen here
----------------------------------------------------------
ID 1A26_HUMAN STANDARD; PRT; 365 AA.
AC P30450; O02963; O78073; P79563; Q30208; Q31623;
Q95377; Q9BD15;
AC Q9BD19; Q9MW42; Q9TQK5;
----------------------------------------------------------
I tried this bit of code, but it only gives me the 1st
accession number it finds - P15456 from the 1st
example - but I want to get both P15646 and Q9SAW0;
------------------------------------------------------------------
use strict;
use Bio::SeqIO;
my $sp_file = shift @ARGV or die$!;
my $seqio_object = Bio::SeqIO->new(-file => $sp_file,
-format => "swiss");
while (my $seq_object = $seqio_object->next_seq) {
print "Accession:
",$seq_object->accession_number(), "\n";
}
------------------------------------------------------------------
Is there a way around?
Thanks in advance.
Anand
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