104 lines
1.8 KiB
Perl
104 lines
1.8 KiB
Perl
#!/usr/bin/env perl
|
|
|
|
use strict;
|
|
use warnings;
|
|
|
|
use FindBin;
|
|
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;
|
|
}
|