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#!/usr/bin/env perl
=pod
=head1 NAME
extract_FL_subset.pl
=head1 USAGE
Required:
--transcripts, -t <string> transcripts.fasta
--gff3, -g <string> transcripts.fasta.transdecoder.gff3
=cut
use strict;
use warnings;
use FindBin;
use Pod::Usage;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use Data::Dumper;
use File::Basename;
use lib ("$FindBin::RealBin/../PerlLib");
use Gene_obj;
my $UTIL_DIR = "$FindBin::RealBin";
my $help;
my $transcripts_file;
my $gff3_file;
&GetOptions( 'transcripts|t=s' => \$transcripts_file,
'gff3|g=s' => \$gff3_file,
'h' => \$help,
);
pod2usage(-verbose => 2, -output => \*STDERR) if ($help || ! ($transcripts_file && $gff3_file));
if (@ARGV) {
die "Error, don't understand options: @ARGV";
}
main: {
my $output_prefix = basename($transcripts_file);
# get the FL entries:
my $FL_accs_file = "$output_prefix.complete_only";
my $cmd = "$UTIL_DIR/get_FL_accs.pl $gff3_file > $FL_accs_file";
&process_cmd($cmd);
# index the current gff file:
$cmd = "$UTIL_DIR/index_gff3_files_by_isoform.pl $gff3_file";
&process_cmd($cmd);
# retrieve the best entries:
my $complete_gff3_filename = $FL_accs_file . ".gff3";
$cmd = "$UTIL_DIR/gene_list_to_gff.pl $FL_accs_file $gff3_file.inx > $FL_accs_file.gff3";
&process_cmd($cmd);
##############################
## Generate the final outputs.
##############################
{
## write final outputs:
$gff3_file = "$FL_accs_file.gff3";
## make a BED file for viewing in IGV
my $bed_file = $gff3_file;
$bed_file =~ s/\.gff3$/\.bed/;
$cmd = "$UTIL_DIR/gff3_file_to_bed.pl $gff3_file > $bed_file";
&process_cmd($cmd);
# make a peptide file:
my $best_pep_file = $gff3_file;
$best_pep_file =~ s/\.gff3$/\.pep/;
$cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file > $best_pep_file";
&process_cmd($cmd);
# make a CDS file:
my $best_cds_file = $best_pep_file;
$best_cds_file =~ s/\.pep$/\.cds/;
$cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file CDS > $best_cds_file";
&process_cmd($cmd);
# make a CDS file:
my $best_cdna_file = $best_pep_file;
$best_cdna_file =~ s/\.pep$/\.mRNA/;
$cmd = "$UTIL_DIR/gff3_file_to_proteins.pl $gff3_file $transcripts_file cDNA > $best_cdna_file";
&process_cmd($cmd);
}
print STDERR "Done. See output files $FL_accs_file.\*\n\n\n";
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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