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
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 chrysalis_component_listing.txt min_seq_length\n\n";
my $comp_list_file = $ARGV[0] or die $usage;
my $min_seq_length = $ARGV[1] or die $usage;
main: {
my $ret_val = 0;
my %seen;
open (my $fh, $comp_list_file) or die "Error, cannot open file $comp_list_file";
while (<$fh>) {
chomp;
my ($comp_id, $comp_base) = split(/\t/);
my $butterfly_fasta_file = "$comp_base.graph.allProbPaths.fasta";
if (-e $butterfly_fasta_file) {
my $fasta_reader = new Fasta_reader($butterfly_fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $sequence = $seq_obj->get_sequence();
if (length($sequence) >= $min_seq_length) {
if ($seen{$sequence}) {
print STDERR "-duplicate sequence detected, excluding it.\n";
next;
}
else {
$seen{$sequence} = 1;
}
print $seq_obj->get_FASTA_format();
}
}
}
else {
print STDERR "Error, no fasta file reported as: $butterfly_fasta_file\n";
$ret_val = 1;
}
}
close $fh;
exit($ret_val);
}
|
