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