[Bioperl-l] Extract contigs

[Paul Cantalupo]

Hello,

You ask "how...extract only contigs with *exact* names" (emphasis mine).
Therefore, change the pattern-match-operator (=~) to an equality operator
'eq' and it should work for you. LMK if you have any more problems.

Best,

Paul



Paul Cantalupo
University of Pittsburgh


On Sun, Apr 27, 2014 at 1:04 PM, Antony03 <antony.vincent.1 at ulaval.ca>wrote:

> Hi,
>
> I wrote this little code:
> #!/usr/bin/perl
>      #By Antony Vincent#
>
>
>
> use strict;
> use warnings;
> use diagnostics;
>
> use Bio::Perl;
> use Bio::SeqIO;
> use IO::String;
> use Bio::SearchIO;
> use Getopt::Long;
>
> my $filename;
> my $help;
>
>
> GetOptions(
>     'file=s' => \$filename,
>     'help!' => \$help,
> ) or die "Incorrect usage! Try perl new_db.pl -help for an exhaustif
> help.\n";
>
> if( $help ) {
>     print "     **********\n";
>     print "     ***HELP***\n";
>     print "     **********\n\n";
>     print "One option is required:\n\n";
>     print "     -file: Your file in multi-fasta\n\n";
>     exit;
> }
> my @taxa_name;
> open(FILE, "<", "test");
>
> while(<FILE>) {
>   chomp;
>   push(@taxa_name, $_);
>
> }
>
> close(FILE);
>
> print @taxa_name;
>
> mkdir 'new_db';
>
>
> my $gb = Bio::SeqIO->new(-file => "<$filename",
>                               -format => "fasta");
>
> my $fa = Bio::SeqIO->new(-file => ">new_db/$filename",
>                               -format => "fasta",
>                               -flush => 0);
>
> SEQ:
> while (my $seq = $gb->next_seq) {
>     my $id_and_desc = $seq->id . " " . $seq->desc;
>     foreach my $str (@taxa_name) {
>         if ($id_and_desc =~ /\Q$str\E/) {
>             $fa->write_seq($seq);
>             next SEQ;
>         }
>     }
> }
>
> It allows to extract contigs from a multi-fasta file. The problem is when I
> try to extract the contig-1, it extracts contig-1, contig-10, contig-11
> ....
>
> How can I change my code for extract only contigs with exact names.
>
> Thanks
>
>
>
> --
> View this message in context:
> http://bioperl.996286.n3.nabble.com/Extract-contigs-tp17469.html
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