changeset 2:28d2dd0f048b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/velvet_optimiser_wrapper_vlsci.pl	Tue Feb 05 19:19:37 2013 -0500
@@ -0,0 +1,154 @@
+#!/usr/bin/perl
+
+#  velvet_optimiser_vlsci.pl
+#  
+#  Copyright 2012 Simon <simon@Hyperion>
+#  
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#  
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#  
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#  MA 02110-1301, USA.
+#  
+#  
+
+use strict;
+use warnings;
+use File::Copy;
+
+my @stuff = @ARGV;
+my %counts;
+my %shortMPs;
+my @reads;
+my $threadsToUse = 2;   #According to Enis, this is the default number of threads that multithreaded programs use..
+
+#TO DO! get velvet compile parameters!
+
+foreach my $param (@stuff){
+    if($param =~ m/galaxy\.datatypes/){
+        $param =~m/datatypes\..+\.(.+)\s+object/;
+        my $type = lc($1);
+        print "$type\n";
+    }
+    else {
+        print $param . "\n";
+    }
+}
+
+#try and split some of it up..
+#kmer stuff
+my $sk = shift @stuff;
+my $ek = shift @stuff;
+my $xk = shift @stuff;
+
+#TO DO! do checks etc on this stuff here!
+
+#get the read file stuff
+my $i = 0;
+
+while(!($stuff[0] =~ m/other:/)){
+    my $index = shift @stuff;
+    my $read_type = shift @stuff;
+    my $sep = shift @stuff;
+    my $file_type = shift @stuff;
+    $file_type =~m/datatypes\..+\.(.+)\s+object/;
+    $file_type = lc($1);
+    $file_type = "fastq" if $file_type =~ m/fastq/i;
+    $counts{$read_type} ++;
+    my $ffile = shift @stuff;
+    my $rfile = shift @stuff if $sep eq "True";
+    my $sMP = shift @stuff;
+    $reads[$i] = "-$read_type";
+    $reads[$i] .= $counts{$read_type} if $counts{$read_type} > 1;
+    if ($sMP eq "shortMP_lib"){
+        my $temp = "-shortMatePaired";
+        $temp .= $counts{$read_type} if $counts{$read_type} > 1;
+        $shortMPs{$temp} = 1;
+    }
+    $reads[$i] .= " -$file_type";
+    $reads[$i] .= " -separate" if $sep eq "True";
+    $reads[$i] .= " $ffile";
+    $reads[$i] .= " $rfile" if $sep eq "True";
+    $i ++;
+}
+
+#get the other stuff
+shift @stuff if $stuff[0] =~ m/other:/;
+my $amos = shift @stuff;
+my $verbose = shift @stuff;
+
+#get the advanced stuff if it exists!
+my ($oFK, $oFC, $vgO, $minC, $maxC);
+if ($stuff[0] =~ m/advanced:/) {
+    shift @stuff;
+    $oFK = shift @stuff;
+    $oFC = shift @stuff;
+    $vgO = shift @stuff;
+    $minC = shift @stuff;
+    $maxC = shift @stuff;
+}
+
+#get the output file names!
+my $contigs_outfile = shift @stuff;
+my $stats_outfile = shift @stuff;
+my $afg_outfile = shift @stuff if $amos eq "amos";
+my $logfile = shift @stuff;
+my $stderr = shift @stuff;
+my $lgraph = shift @stuff;
+
+#build the command line...
+
+my $cmd = "VelvetOptimiser.pl -d temp_vgo_files -s $sk -e $ek -x $xk";
+$cmd .= " -a" if($amos eq "amos");
+$cmd .= " -v" if($verbose eq "verbose");
+
+$cmd .= " -f '";
+foreach my $line (@reads){
+    $cmd .= " $line";
+}
+$cmd .= "'";
+
+my $vgopt = $vgO;
+foreach my $key(keys %shortMPs){
+    $vgopt .= " $key" if $key;
+}
+
+$cmd .= " -o '$vgopt'" if $vgopt;
+
+$cmd .= " -k $oFK" if $oFK;
+$cmd .= " -c $oFC" if $oFC;
+$cmd .= " -m $minC" if $minC;
+$cmd .= " -z $maxC" if $maxC;
+$cmd .= " -t $threadsToUse";
+
+$cmd .= " 2> $stderr";
+
+print "\n$cmd\n";
+
+print "about to run the command!";
+
+if(system($cmd) == 0) {
+    #copy the files to the new places and delete the directory..
+    print "Copying output\n";
+    copy("temp_vgo_files/contigs.fa", $contigs_outfile);
+    copy("temp_vgo_files/stats.txt", $stats_outfile);
+    copy(glob("temp_vgo_files/*Logfile.txt"), $logfile);
+    copy("temp_vgo_files/velvet_asm.afg", $afg_outfile) if $amos eq "amos";
+    copy("temp_vgo_files/LastGraph", $lgraph);
+    system("rm -rf temp_vgo_files") == 0 or die "Couldn't delete temporary directory. $!";
+}
+else {
+    print "There was a velvet optimiser error\n";
+    exit(1);
+}
+
+exit(0);