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#!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
use FindBin;
my $usage = "usage: $0 file.fasta [max_genes]\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $max_genes = $ARGV[1];
main: {
my $sim_out_dir = "sim_AS_data";
unless (-d $sim_out_dir) {
mkdir $sim_out_dir or die $!;
}
my $fasta_reader = new Fasta_reader($fasta_file);
my %gene_to_seqs;
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my ($trans, $gene) = split(/;/, $acc);
unless ($gene) {
die "Error, need trans;gene format for accession: $acc";
}
my $sequence = $seq_obj->get_sequence();
push (@{$gene_to_seqs{$gene}}, { acc => $acc,
seq => $sequence, });
}
my $gene_counter = 0;
## only including those entries that are alt-spliced
foreach my $gene (keys %gene_to_seqs) {
my @trans = @{$gene_to_seqs{$gene}};
if (scalar @trans == 1) {
next;
}
my $outdir = $gene;
$outdir =~ s/\W/_/g;
mkdir ("$sim_out_dir/$outdir") or die $!;
my $template_file = "$sim_out_dir/$outdir/$outdir.template.fa";
open (my $ofh, ">$template_file") or die "Error, cannot write to $template_file";
foreach my $entry (@trans) {
my ($acc, $sequence) = ($entry->{acc}, $entry->{seq});
print $ofh ">$acc\n$sequence\n";
}
close $ofh;
my $outfile = "$sim_out_dir/$outdir/$outdir.reads.fa";
my $cmd = "$FindBin::RealBin/../simulate_illuminaPE_from_transcripts.pl --transcripts $template_file --SS > $outfile";
&process_cmd($cmd);
$gene_counter++;
if ($max_genes && $gene_counter >= $max_genes) {
last;
}
}
exit(0);
}
####
sub process_cmd {
my ($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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