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|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
####################################################################################
#
# usage: $0 --reads_list_file <string> --out_token <string> [Trinity params]
#
# Required:
#
# --reads_list_file <string> file containing list of filenames corresponding
# to the reads.fasta
#
# --out_token <string> token added to the output file name
#
#####################################################################################
# Example:
#
# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar ~/SVN/trinityrnaseq/trunk/Butterfly/Butterfly.jar --JM 1G --seqType fa
__EOUSAGE__
;
my $reads_file;
my $help_flag;
my $out_token = "";
&GetOptions (
'reads_list_file=s' => \$reads_file,
'h' => \$help_flag,
'out_token=s' => \$out_token,
);
my @TRIN_ARGS = @ARGV;
if ($help_flag) {
die $usage;
}
unless ($reads_file && -s $reads_file) {
die $usage;
}
unless ($out_token) {
die $usage;
}
my $trin_args = join(" ", @TRIN_ARGS);
open (my $fh, $reads_file) or die "Error, cannot open file $reads_file";
while (<$fh>) {
chomp;
my @x = split(/\s+/);
my $file = pop @x;
my $cmd = "$FindBin::RealBin/../../../Trinity --single \"$file\" --output \"$file.trinity.$out_token\" $trin_args ";
print "$cmd\n";
}
exit(0);
|
