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
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "usage: $0 transcripts.cdna.fasta\n\n";
my $transcripts_fasta = $ARGV[0] or die $usage;
my $graphs_per_dir = 100;
main: {
my $fasta_reader = new Fasta_reader($transcripts_fasta) or die $!;
my $count = 0;
while (my $seq_obj = $fasta_reader->next()) {
my $accession = $seq_obj->get_accession();
$accession =~ s/\W/_/g;
my $sequence = $seq_obj->get_sequence();
my $dir_no = int($count/$graphs_per_dir);
my $outdir = "trans_graphs/g_$dir_no";
if (! -d $outdir) {
&process_cmd("mkdir -p $outdir");
}
my $fa_file = "$outdir/$accession.fa";
open (my $ofh, ">$fa_file") or die $!;
print $ofh ">$accession\n$sequence\n";
close $ofh;
my $cmd = "~/SVN/trinityrnaseq/trunk/util/misc/Monarch --misc_seqs $fa_file --graph $fa_file.dot";
&process_cmd($cmd);
$count++;
}
print STDERR "\n\nDone.\n\n";
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
|
