1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
|
#!/usr/bin/env perl
#
# Extract fast5 file names from a poretools fasta file and prepend an index to uniquify names
#
use strict;
use Bio::Perl;
use Getopt::Long;
my $inFile = Bio::SeqIO->new(-file => $ARGV[0], '-format' => 'Fasta');
my $outFile = Bio::SeqIO->new(-fh => \*STDOUT, '-format' => 'Fasta');
open(FM, ">consensus_fast5.fofn");
my $id = 0;
while(my $seq = $inFile->next_seq())
{
my $in_name = $seq->display_id();
my $out_name = "$id.$in_name";
my $desc = $seq->desc();
print FM "$desc\n";
$seq->display_id($out_name);
$outFile->write_seq($seq);
$id++;
}
|
