perl script

[sainath]

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[Transient]

What have you tried thus far?

You'd probably want to take a look at using split to gather what you need.

[citromatik]

perl -lne '/gi\|(\d+)\|/ && push @sofar,$1}{$,=",";print @sofar' <yourfile>

[ack]

I used a similar idea but did as follows:

my $file = '...the OPs File example..." #used as a string
                                        # to simplify my
                                        # test
my @gi_ids = $file =~/gi\|(\d+)\|/g;

That leaves the list @gi_ids containing all of the gi id's that were in the string (i.e., it finds 4 gi id's in the OPs example).

Just another possible strategy. It looks to me like all of the respondents' ideas would work fine. Mine is just another variation.

Hope that helps.

[leslie]

Hi firend,


You can use this code..,

use strict;
use warnings;
use Data::Dumper;
my($File,$FILE_FH,$data,@total_data,$new,@gi);
$File="./fasta.txt";
open  $FILE_FH, '<', $File or die "Failed to Open File $File for $!";
 $data=<$FILE_FH>;
 @total_data=split(/gi\|(\d+)\|/,$data);
foreach $new(@total_data)
{
    push @gi,$new if($new =~ /^\d+$/);
}
print Dumper @gi;