Mercurial > repos > simon-gladman > velvet_optimiser

comparison velvet_optimiser_wrapper_vlsci.pl @ 2:28d2dd0f048b draft

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author simon-gladman
date Tue, 05 Feb 2013 19:19:37 -0500
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1:94dbee11c8a9 2:28d2dd0f048b
1 #!/usr/bin/perl
2
3 # velvet_optimiser_vlsci.pl
4 #
5 # Copyright 2012 Simon <simon@Hyperion>
6 #
7 # This program is free software; you can redistribute it and/or modify
8 # it under the terms of the GNU General Public License as published by
9 # the Free Software Foundation; either version 2 of the License, or
10 # (at your option) any later version.
11 #
12 # This program is distributed in the hope that it will be useful,
13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 # GNU General Public License for more details.
16 #
17 # You should have received a copy of the GNU General Public License
18 # along with this program; if not, write to the Free Software
19 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
20 # MA 02110-1301, USA.
21 #
22 #
23
24 use strict;
25 use warnings;
26 use File::Copy;
27
28 my @stuff = @ARGV;
29 my %counts;
30 my %shortMPs;
31 my @reads;
32 my $threadsToUse = 2; #According to Enis, this is the default number of threads that multithreaded programs use..
33
34 #TO DO! get velvet compile parameters!
35
36 foreach my $param (@stuff){
37 if($param =~ m/galaxy\.datatypes/){
38 $param =~m/datatypes\..+\.(.+)\s+object/;
39 my $type = lc($1);
40 print "$type\n";
41 }
42 else {
43 print $param . "\n";
44 }
45 }
46
47 #try and split some of it up..
48 #kmer stuff
49 my $sk = shift @stuff;
50 my $ek = shift @stuff;
51 my $xk = shift @stuff;
52
53 #TO DO! do checks etc on this stuff here!
54
55 #get the read file stuff
56 my $i = 0;
57
58 while(!($stuff[0] =~ m/other:/)){
59 my $index = shift @stuff;
60 my $read_type = shift @stuff;
61 my $sep = shift @stuff;
62 my $file_type = shift @stuff;
63 $file_type =~m/datatypes\..+\.(.+)\s+object/;
64 $file_type = lc($1);
65 $file_type = "fastq" if $file_type =~ m/fastq/i;
66 $counts{$read_type} ++;
67 my $ffile = shift @stuff;
68 my $rfile = shift @stuff if $sep eq "True";
69 my $sMP = shift @stuff;
70 $reads[$i] = "-$read_type";
71 $reads[$i] .= $counts{$read_type} if $counts{$read_type} > 1;
72 if ($sMP eq "shortMP_lib"){
73 my $temp = "-shortMatePaired";
74 $temp .= $counts{$read_type} if $counts{$read_type} > 1;
75 $shortMPs{$temp} = 1;
76 }
77 $reads[$i] .= " -$file_type";
78 $reads[$i] .= " -separate" if $sep eq "True";
79 $reads[$i] .= " $ffile";
80 $reads[$i] .= " $rfile" if $sep eq "True";
81 $i ++;
82 }
83
84 #get the other stuff
85 shift @stuff if $stuff[0] =~ m/other:/;
86 my $amos = shift @stuff;
87 my $verbose = shift @stuff;
88
89 #get the advanced stuff if it exists!
90 my ($oFK, $oFC, $vgO, $minC, $maxC);
91 if ($stuff[0] =~ m/advanced:/) {
92 shift @stuff;
93 $oFK = shift @stuff;
94 $oFC = shift @stuff;
95 $vgO = shift @stuff;
96 $minC = shift @stuff;
97 $maxC = shift @stuff;
98 }
99
100 #get the output file names!
101 my $contigs_outfile = shift @stuff;
102 my $stats_outfile = shift @stuff;
103 my $afg_outfile = shift @stuff if $amos eq "amos";
104 my $logfile = shift @stuff;
105 my $stderr = shift @stuff;
106 my $lgraph = shift @stuff;
107
108 #build the command line...
109
110 my $cmd = "VelvetOptimiser.pl -d temp_vgo_files -s $sk -e $ek -x $xk";
111 $cmd .= " -a" if($amos eq "amos");
112 $cmd .= " -v" if($verbose eq "verbose");
113
114 $cmd .= " -f '";
115 foreach my $line (@reads){
116 $cmd .= " $line";
117 }
118 $cmd .= "'";
119
120 my $vgopt = $vgO;
121 foreach my $key(keys %shortMPs){
122 $vgopt .= " $key" if $key;
123 }
124
125 $cmd .= " -o '$vgopt'" if $vgopt;
126
127 $cmd .= " -k $oFK" if $oFK;
128 $cmd .= " -c $oFC" if $oFC;
129 $cmd .= " -m $minC" if $minC;
130 $cmd .= " -z $maxC" if $maxC;
131 $cmd .= " -t $threadsToUse";
132
133 $cmd .= " 2> $stderr";
134
135 print "\n$cmd\n";
136
137 print "about to run the command!";
138
139 if(system($cmd) == 0) {
140 #copy the files to the new places and delete the directory..
141 print "Copying output\n";
142 copy("temp_vgo_files/contigs.fa", $contigs_outfile);
143 copy("temp_vgo_files/stats.txt", $stats_outfile);
144 copy(glob("temp_vgo_files/*Logfile.txt"), $logfile);
145 copy("temp_vgo_files/velvet_asm.afg", $afg_outfile) if $amos eq "amos";
146 copy("temp_vgo_files/LastGraph", $lgraph);
147 system("rm -rf temp_vgo_files") == 0 or die "Couldn't delete temporary directory. $!";
148 }
149 else {
150 print "There was a velvet optimiser error\n";
151 exit(1);
152 }
153
154 exit(0);