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|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE;
#################################################
#
# usage: $0 [opts] < trinity_fasta_files_listing
#
#################################################
#
# Required
#
# --token_prefix <string> eg. TRINITY_DN or TRINITY_GG
#
# --output_prefix <string> eg. Trinity or Trinity_GG
#
# Optional:
#
# --include_supertranscripts flag, captures the supertranscripts fasta and gtf
#
##################################################
__EOUSAGE
;
my $token_prefix;
my $output_prefix;
my $include_supertranscripts_flag;
&GetOptions ( 'h' => \$help_flag,
'token_prefix=s' => \$token_prefix,
'output_prefix=s' => \$output_prefix,
'include_supertranscripts' => \$include_supertranscripts_flag,
);
if ($help_flag) {
die $usage;
}
unless ($token_prefix && $output_prefix) {
die $usage;
}
my $ofh_trinity_fasta;
open($ofh_trinity_fasta, ">$output_prefix.fasta") or die "Error, cannot write to $output_prefix.fasta";
my $ofh_supertrans_fasta;
my $ofh_supertrans_gtf;
if ($include_supertranscripts_flag) {
open($ofh_supertrans_fasta, ">$output_prefix.SuperTrans.fasta") or die $!;
open($ofh_supertrans_gtf, ">$output_prefix.SuperTrans.gtf") or die $!;
}
main: {
while (<STDIN>) {
my $filename = $_;
chomp $filename;
unless (-e $filename) {
print STDERR "ERROR, filename: $filename is indicated to not exist.\n";
next;
}
if (-s $filename) {
# ie. read_partitions/Fb_0/CBin_161/c16167.trinity.reads.fa
$filename =~ m|c(\d+)\.trinity\.reads| or die "Error, cannot parse Trinity component value from filename: $filename";
my $component = $1;
&process_files($filename, $component);
}
}
exit(0);
}
####
sub process_files {
my ($filename, $component) = @_;
{
# write fasta
open (my $fh, $filename) or die "Error, cannot open file $filename";
while (<$fh>) {
if (/>/) {
s/>/>${token_prefix}${component}\_/;
}
print $ofh_trinity_fasta $_;
}
close $fh;
}
if ($include_supertranscripts_flag) {
# write supertranscripts
my $core_filename = $filename;
$core_filename =~ s/\.fasta$//;
{ # supertranscripts fasta:
my $supertranscripts_fasta = "$core_filename.SuperTrans.fasta";
if (! -s $supertranscripts_fasta) {
die "Error, missing file: $supertranscripts_fasta";
}
open(my $fh, $supertranscripts_fasta) or die "Error, cannot open file: $supertranscripts_fasta";
while (<$fh>) {
if (/>/) {
s/>/>${token_prefix}${component}\_/;
}
print $ofh_supertrans_fasta $_;
}
close $fh;
}
{
# supertranscripts gtf
my $supertranscripts_gtf = "$core_filename.SuperTrans.gtf";
if (! -s $supertranscripts_gtf) {
die "Error, missing file: $supertranscripts_gtf";
}
open(my $fh, $supertranscripts_gtf) or die "Error, cannot open file $supertranscripts_gtf";
while (<$fh>) {
my $line = $_;
if (/\w/) {
my @x = split(/\t/, $line);
my $id = $x[0];
$line =~ s/$id/${token_prefix}${component}_${id}/g;
}
print $ofh_supertrans_gtf $line;
}
close $fh;
}
}
return;
}
|
