[Bioperl-l] script

[Brian Osborne]

Lobvi,

If you really mean "proteins" and for some reason there may be both protein
and nucleotide sequences in your file then something like:

~>perl -e 'use Bio::SeqIO; $in = Bio::SeqIO->new(-file => $ARGV[0]); while
($seq = $in->next_seq ){ $count++ if ($seq->alphabet eq "protein") } print
$count;' test.fa


Otherwise, the grep.

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 Lobvi Matamoros
Sent: Thursday, September 04, 2003 1:58 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] script


Hi:

Does any one have an script to count how many proteins do you have in a
database/file in FASTA format

Thanks in advance for your help

Lobvi

Lobvi Matamoros Fernández, Ph.D
Post-doctoral fellow

Centre de Recherche du CHUL
2705 Boul. Laurier, T3-80
Sainte-Foy (Québec)
G1V 4G2 CANADA
Tel: 418-6542261
FAX:418-654-2279

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