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#!/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_file = $ARGV[0] or die $usage;
my $graphs_per_dir = 100;
main: {
my $fasta_reader = new Fasta_reader($transcripts_fasta_file) or die $!;
my $count = 0;
my %gene_to_seq;
while (my $seq_obj = $fasta_reader->next()) {
my $accession = $seq_obj->get_accession();
my $sequence = $seq_obj->get_sequence();
my ($trans, $gene) = split(/;/, $accession);
$gene_to_seq{$gene}->{$trans} = $sequence;
}
foreach my $gene (keys %gene_to_seq) {
my $trans_href = $gene_to_seq{$gene};
my @trans = keys %$trans_href;
unless (scalar @trans > 1) {
# want just alt-splice ones.
next;
}
$gene =~ s/\W/_/g;
my $dir_no = int($count/$graphs_per_dir);
my $outdir = "gene_altSplice_graphs/g_$dir_no";
if (! -d $outdir) {
&process_cmd("mkdir -p $outdir");
}
my $fa_file = "$outdir/$gene.fa";
open (my $ofh, ">$fa_file") or die $!;
foreach my $trans_acc (keys %$trans_href) {
my $seq = $trans_href->{$trans_acc};
print $ofh ">$trans_acc\n$seq\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;
}
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