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|
#!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
my $usage = <<_EOUSAGE_;
##################################################################
#
# Required:
#
# --target <string> : transcript sequences (eg. 'Trinity.fasta')
#
# If paired reads:
#
# --left <string> :left reads
# --right <string> :right reads
#
# Or, if unpaired reads:
#
# --single <string> :single reads
#
#
# --paired_fragment_length <int> :size of a read pair insert (def=300)
#
#
#############################################################################################################
_EOUSAGE_
;
my ($target_fasta, $left_file, $right_file, $single_file, $SS_lib_type, $paired_fragment_length);
# defaults:
$paired_fragment_length = 300;
&GetOptions(
## general opts
"target_fasta=s" => \$target_fasta,
"left=s" => \$left_file,
"right=s" => \$right_file,
"single=s" => \$single_file,
"SS_lib_type=s" => \$SS_lib_type,
"paired_fragment_length=i" => \$paired_fragment_length,
);
## Check options set:
unless ( ($left_file && $right_file) || $single_file) {
die $usage;
}
main: {
my $cmd = "ln -s $target_fasta TARGET.fa";
&process_cmd($cmd) unless (-e "TARGET.fa");
$cmd = "bowtie-build TARGET.fa TARGET";
&process_cmd($cmd) unless (-s "TARGET.1.ebwt");
if ($left_file && $right_file) {
$cmd = "tophat --bowtie1 -i 5 -r $paired_fragment_length TARGET $left_file $right_file";
&process_cmd($cmd);
}
else {
$cmd = "tophat --bowtie1 -i 5 TARGET $single_file";
&process_cmd($cmd);
}
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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