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4
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1 use strict;
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2 use warnings;
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3 use File::Basename;
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4 use Cwd;
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5 use File::Path qw(make_path remove_tree);
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6 die qq(
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7 Bad numbr of inputs
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8
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9 ) if(!@ARGV);
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10
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11 my @bam_list_entries;
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12
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13 my $player_options = "--bowtie2 -p 4 ";
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14 my $bam_output;
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15 my $summary;
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16 my $genome;
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17 my $singles = "";
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18 my $mates1 = "";
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19 my $mates2 = "";
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20 my $directional="";
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21 my $format="";
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22 my $log_file="";
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23
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24
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25 foreach my $input (@ARGV)
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26 {
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27 my @tmp = split "::", $input;
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28 if($tmp[0] eq "GENOME")
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29 {
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30 $genome=$tmp[1];
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31 }
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32 elsif($tmp[0] eq "MATES")
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33 {
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34 $mates1 = $tmp[1];
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35 $mates2 = $tmp[2];
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36 }
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37 elsif($tmp[0] eq "SINGLES")
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38 {
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39 $singles = $tmp[1];
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40 }
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41 elsif($tmp[0] eq "FORMAT")
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42 {
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43 $format = $tmp[1];
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44 }
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45 elsif($tmp[0] eq "DIRECTIONAL")
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46 {
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47 $directional = $tmp[1];
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48 }
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49 elsif($tmp[0] eq "SUMMARY")
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50 {
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51 $summary = $tmp[1];
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52 }
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53 elsif($tmp[0] eq "OUTPUT")
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54 {
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55 $bam_output = $tmp[1];
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56 }
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57
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58 else
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59 {
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60 die("Unknown Input: $input\n");
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61 }
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62 }
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63
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64
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65 my $working_dir = cwd()."/BISMARK_OUTPUT";
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66 make_path($working_dir);
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67
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68
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69 #run bismark
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70
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71 if ($singles eq "")
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72 {
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73 system ("bismark $player_options $directional $format $genome -o $working_dir -1 $mates1 -2 $mates2 > $summary 2>&1 ");
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74
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75 }
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76 else
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77 {
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78 system ("bismark $player_options $directional $format $genome -o $working_dir $singles > $summary 2>&1");
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79
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80 }
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81
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82
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83 move_files($working_dir);
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84
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85
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86 sub move_files
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87 {
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88 my $name;
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89 my $suffix;
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90 my $path;
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91 my $local_dir = $_[0];
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92 opendir(DIR, $local_dir);
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93 #print ("Openning: $local_dir\n");
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94 my @FILES= readdir(DIR);
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95 closedir(DIR);
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96 foreach my $file (@FILES)
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97 {
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98 if ($file eq "." || $file eq "..")
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99 {
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100 #print ("./ or ../ skipped\n");
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101 }
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102 elsif (-d "$local_dir/$file")
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103 {
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104 #print ("moving to: $local_dir/$file\n");
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105 move_files("$local_dir/$file");
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106 }
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107 elsif (-f "$local_dir/$file")
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108 {
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109 ($name,$path,$suffix) = fileparse($file,qr"\.[^.]*$");
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110 if ($suffix eq ".sam")
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111 {
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112 #converto to BAM and Delete SAM
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113 system ("MergeSamFiles.sh MAX_RECORDS_IN_RAM=2000000 I=$local_dir/$file O=$bam_output VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true > /dev/null 2>&1");
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114 system ("rm -rf $local_dir/$file");
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115
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116 }
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117 elsif($suffix eq ".txt")
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118 {
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119 system ("mv $local_dir/$file $summary");
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120 }
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121 }
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122 else
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123 {
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124 die("Unrecognized file generated: $file\n");
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125 }
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126
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127 }
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128 }
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129
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130
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131
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132
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133
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