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1 #!/usr/bin/env perl
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2 ## A wrapper script to call chewBBACA.py and collect its output
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3 use strict;
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4 use warnings;
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5 use Cwd;
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6 use English;
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7 use File::Copy;
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8 use File::Basename;
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9
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10 # Parse arguments
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11 my ($myFunction,
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12 $input1,
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13 $input1_names,
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14 $output,
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15 $python) = @ARGV;
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16
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17 # Run program
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18 my $abs_path = Cwd::abs_path($PROGRAM_NAME);
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19 my $scriptdir = dirname($abs_path);
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20
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21 prepareEnvironment($input1,$input1_names,"input_dir");
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22 runChewBBACA();
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23 collectOutput();
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24 exit(0);
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25
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26 # Run chewBBACA
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27 sub runChewBBACA {
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28 my $abs_path = Cwd::abs_path($PROGRAM_NAME);
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29 my $scriptdir = dirname($abs_path);
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30 my $createschemadir = "$scriptdir/createschema";
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31 my $allelecalldir = "$scriptdir/allelecall";
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32 my $SchemaEvaluatordir = "$scriptdir/SchemaEvaluator";
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33 my $utilsdir = "$scriptdir/utils";
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34 my $newpath = "PATH=$ENV{PATH}:$createschemadir:$allelecalldir:$SchemaEvaluatordir:$utilsdir";
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35 my $result = system("$newpath; $python");
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36 return 0;
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37 }
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38
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39 # Run prepareEnvironment, create the directory $indir with symlinks to the files listed in $inlist
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40 sub prepareEnvironment {
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41 my ($inlist, $inlist_names, $indir) = @_;
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42 if ($inlist ne "NULL") {
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43 mkdir($indir);
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44 my @inputs = split(',', $inlist);
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45 if ($inlist_names ne "NULL") {
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46 my @inputs_names = split(',', $inlist_names);
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47 for my $i ( 0 .. $#inputs ){
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48 my $name = $inputs_names[$i];
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49 $name =~ s/ /_/g;
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50 $name =~ s/\//_/g;
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51 $name =~ s/\(/_/g;
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52 $name =~ s/\)/_/g;
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53 $name =~ s/\[/_/g;
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54 $name =~ s/\]/_/g;
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55 $name =~ s/\{/_/g;
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56 $name =~ s/\}/_/g;
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57 symlink($inputs[$i], $indir . "/" . $name);
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58 }
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59 }
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60 else {
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61 foreach my $i (@inputs){
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62 symlink($i, $indir . "/" . basename($i));
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63 }
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64 }
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65 }
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66 return 0;
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67 }
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68
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69 # Collect output
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70 sub collectOutput{
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71 # CreateSchema
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72 if ($myFunction eq "CreateSchema") {
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73 my($dataname, $datadir, $datasuffix) = fileparse($output,qr/\.[^.]*/);
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74 my @fasta_files = glob "output_dir/*.fasta";
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75 my $dest_dir = $datadir . $dataname . "/";
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76 mkdir($dest_dir);
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77 open(my $fh1, '>', $output) or die "Could not open file '$output' $!";
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78 my $new_fasta_file = "";
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79 foreach my $fasta_file (@fasta_files) {
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80 $new_fasta_file = $dest_dir . basename($fasta_file);
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81 print $fh1 "$new_fasta_file\n";
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82 move($fasta_file, $new_fasta_file) or die "Could not move $fasta_file: $!\n";
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83 }
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84 close $fh1;
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85 my @short_fasta_files = glob "output_dir/short/*.fasta";
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86 my $short_dest_dir = $datadir . $dataname . "/short/";
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87 mkdir($short_dest_dir);
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88 foreach my $short_fasta_file (@short_fasta_files) {
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89 move($short_fasta_file, $short_dest_dir) or die "Could not move $short_fasta_file: $!\n";
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90 }
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91 }
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92 # AlleleCall
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93 if ($myFunction eq "AlleleCall") {
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94 my @outputs = split(',', $output);
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95 my @statistics = glob "output_dir/results_*/results_statistics.tsv";
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96 if (@statistics == 1) {
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97 move($statistics[0], $outputs[0])
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98 }
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99 my @contigsinfo = glob "output_dir/results_*/results_contigsInfo.tsv";
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100 if (@contigsinfo == 1) {
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101 move($contigsinfo[0], $outputs[1])
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102 }
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103 my @alleles = glob "output_dir/results_*/results_alleles.tsv";
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104 if (@alleles == 1) {
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105 move($alleles[0], $outputs[2])
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106 }
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107 my @logginginfo = glob "output_dir/results_*/logging_info.txt";
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108 if (@logginginfo == 1) {
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109 move($logginginfo[0], $outputs[3])
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110 }
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111 my @repeatedloci = glob "output_dir/results_*/RepeatedLoci.txt";
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112 if (@repeatedloci == 1) {
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113 move($repeatedloci[0], $outputs[4])
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114 }
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115 }
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116 # SchemaEvaluator
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117 if ($myFunction eq "SchemaEvaluator") {
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118 my($dataname, $datadir, $datasuffix) = fileparse($output,qr/\.[^.]*/);
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119 my @output_files = glob "output_rms/*.*";
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120 my $dest_dir = $dataname . "/";
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121 mkdir($dest_dir);
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122 my $new_output_file = "";
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123 foreach my $output_file (@output_files) {
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124 $new_output_file = $dest_dir . basename($output_file);
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125 move($output_file, $new_output_file) or die "Could not move $output_file: $!\n";
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126 }
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127 open(my $fh2, '<', $dest_dir . "SchemaEvaluator.html") || die "File not found";
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128 my @lines = <$fh2>;
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129 close($fh2);
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130 my @newlines;
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131 foreach(@lines) {
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132 $_ =~ s/\.\.\/\.\.\/\.\.\/.*?\/database\/files\/...\/dataset/dataset/g;
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133 push(@newlines,$_);
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134 }
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135 # write the html to the Galaxy output file
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136 #open($fh2, '>', $output) || die "File not found";
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137 #print $fh2 @newlines;
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138 #close($fh2);
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139 my @html_output_files = glob "output_rms/genes_html/*.*";
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140 my $html_dest_dir = $dest_dir . "genes_html/";
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141 mkdir($html_dest_dir);
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142 foreach my $html_output_file (@html_output_files) {
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143 move($html_output_file, $html_dest_dir) or die "Could not move $html_output_file: $!\n";
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144 }
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145 my $cmd = `tar -cpf $output $dest_dir`;
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146 }
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147 return 0;
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148 }
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149
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