Mercurial > repos > nml > seqtk_nml

annotate seqtk_nml.pl @ 0:e1867440ed36 draft

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planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
author nml
date Tue, 19 Sep 2017 16:37:42 -0400
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0
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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1 #!/usr/bin/env perl
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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2 package seqtk_nml;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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3 use warnings;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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4 use strict;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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5 use Bio::SeqIO;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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6 use Getopt::Long;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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7 use Pod::Usage;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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8 use File::Copy;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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9 __PACKAGE__->run unless caller;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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10
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11
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12 my $rv;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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13
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14 sub get_parameters {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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15 my ($fastaref, $type, $coverage, $length,$log);
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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16 my ($for,$rev,$out_for,$out_rev);
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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17 #determine if our input are as sub arguments or getopt::long
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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18 if ( @_ && $_[0] eq __PACKAGE__ ) {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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19 Getopt::Long::Configure('bundling');
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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20 GetOptions(
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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21 'ref=s' => \$fastaref,
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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22 'type=s' => \$type,
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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23 'forward=s' => \$for,
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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24 'reverse=s' => \$rev,
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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25 'out_forward=s' => \$out_for,
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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26 'out_reverse=s' => \$out_rev,
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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27 'log=s'=> \$log,
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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28 'cov=s' => \$coverage
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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29 );
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30 }
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31
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32 if ( !$for || !( -e $for ) ) {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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33 print "ERROR: Was not given or could not find fastq file: '$for'\n";
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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34 pod2usage( -verbose => 1 );
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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35 }
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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36
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37 if ( !$out_for ) {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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38 print "ERROR: Was not given output file path for fastq\n";
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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39 pod2usage( -verbose => 1 );
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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40 }
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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41
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42 if ( $type eq 'paired') {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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43 if ( !$rev || !( -e $rev ) ) {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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44 print "ERROR: Was not given or could not find reverse fastq file: '$rev'\n";
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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45 pod2usage( -verbose => 1 );
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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46 }
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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47
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48 if ( !$out_rev ) {
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49 print "ERROR: Was not given output file path for reverse fastq\n";
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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50 pod2usage( -verbose => 1 );
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51 }
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52 }
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53
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54 if ( !$coverage ) {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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55 print "ERROR: Was not given a coverage number\n";
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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56 pod2usage( -verbose => 1 );
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57 }
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58
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59 if ( $coverage <=0 ) {
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60 print "ERROR: Was given a coverage less than 0\n";
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61 pod2usage( -verbose => 1 );
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62 }
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63
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64
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65
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66 if ( !$log ) {
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67 print "ERROR: Was not given a log file\n";
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68 pod2usage( -verbose => 1 );
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69 }
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70
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71
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72 return ($fastaref, $type, $coverage, $length, $log,$for,$rev,$out_for,$out_rev);
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73 }
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74
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75
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76 sub run {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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77 my ($fastaref, $type, $coverage, $length, $log,$for,$rev,$out_for,$out_rev) = get_parameters(@_);
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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78 my $subsample_size;
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79
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80
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81 #open log fh here
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82 open my $log_fh,">" ,"$log";
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83
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84
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85 my @in_fastqs;
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86 my @out_fastqs;
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87
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88
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89 if ($type eq "single"){
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90 $in_fastqs[0] = $for;
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91 $out_fastqs[0] = $out_for;
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92 }elsif ($type eq 'paired' ) {
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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93 $in_fastqs[0] = $for;
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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94 $in_fastqs[1] = $rev;
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95 $out_fastqs[0] = $out_for;
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96 $out_fastqs[1] = $out_rev;
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97 }
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98 else {
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99 die "Given unknown read type of '$type'";
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100 }
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101
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102 #get total read lengths from all fastq files given
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103 my $total= get_total_length(@in_fastqs);
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104
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105
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106 if (!($coverage)){
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107 $coverage = 50;
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108 }
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109
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110 my $seq_in = Bio::SeqIO->new(
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111 -format => 'fasta',
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112 -file => $fastaref,
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113 );
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114
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115 while ( my $seq = $seq_in->next_seq()) {
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116 $length += $seq->length();
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117 }
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118
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119
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120 print $log_fh "Downsampling to coverage of: $coverage\n";
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121 print $log_fh "Total number of Basepairs: $total\n";
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122 print $log_fh "Length of Reference: $length\n";
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123
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124 my $rawcoverage = $total/$length;
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125 printf $log_fh "Raw Coverage: %.3f\n",$rawcoverage;
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126
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127 if($rawcoverage > $coverage){
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128 #need to downsample
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129 #calculate $subsample_size
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130 $subsample_size = $coverage/$rawcoverage;
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131 printf $log_fh "subsample: %.3f",$subsample_size;
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132
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133 foreach my $fastq (@in_fastqs){
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134 my $out = shift @out_fastqs;
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135 #seed always set to 42 for reproducibility
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136 my $seqCommand = "seqtk sample -s42 $fastq $subsample_size > $out";
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137 $rv = system($seqCommand);
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138 #need to bit shift 8 bit because seqtk exit code for some reason are greater then standard 0-255 values that most unix application expect
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139 die "Error when running '$seqCommand' command" if $rv >>8;
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140 }
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141 } else {
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142 #no sampling needed, just copy the fastq's to the output
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143 print "Subsampling not required\n";
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144 foreach my $fastq (@in_fastqs){
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145 my $out = shift @out_fastqs;
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146 copy($fastq,$out) || die "Not able to copy '$fastq' to '$out' with error $!";
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147 }
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148 }
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149
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150
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151
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152 }
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153
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154
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155 sub get_total_length {
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156 my (@files) = @_;
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157 my $total;
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158 foreach my $fastq( @files) {
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159
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160 open my $in, "<",$fastq || die "Could not open file '$fastq'";
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161 #skip first 3 lines
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162 for ( 0..2) {
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163 my $line = <$in>;
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164 }
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165
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166 while ( <$in>) {
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167 chomp;
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168 $total+=length($_);
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169 #skip first 3 lines
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170 for ( 0..2) {
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171 my $line = <$in>;
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172 }
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173 }
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174 close $in;
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175
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176
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177 }
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178
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179 return $total;
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180
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181 }
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182
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183 1;
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184
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185
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186 =head1 NAME
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187
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188
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189
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190 seqtk_nml.pl - Down sample fastq(s) if raw coverage is above user provided level
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191
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192
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193 =head1 SYNOPSIS
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194
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195 seqtk_nml.pl --ref reference.fasta --forward first_R1.fastq --reverse --reverse_R2.fastq --out_forward answer_R1.fastq --out_reverse answer_R2.fastq --log log-file
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196
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197
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198 =head1 OPTIONS
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199
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200 =over
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201
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202 =item
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203
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204 =item B<--ref>
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205
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206 Reference fasta file that we getting the expected length [Required]
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207
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208
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209 =item B<--cov>
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210
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211 Coverage desired i.e 50.0
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212
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213
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214 =item B<--forward>
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215
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216 Forward fastq read file. [Required]
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217
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218 =item B<--reverse>
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219
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220 Reverse fastq read file. Can be optional
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221
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222
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223 =item B<--out_forward>
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224
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225 Downsampled forward fastq read file. [Required]
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226
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227 =item B<--out_reverse>
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228
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229 Downsampled reverse fastq read file. Can be optional
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230
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231
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232 =item B<--log>
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233
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234 Log file that indicate what has happen. [Required]
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235
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236 =item B<--type>
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237
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238 Indicate to application if we are receiving one or two fastq files [Required] ['paired','single']
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239
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240
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241
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242 =back
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243
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244 =head1 DESCRIPTION
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245
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246
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247 Downsample fastq(s) reads based on the raw coverage from reference fasta file. Needed when we have too much data to run correctly in downstream analyses tools. i.e spades , snvphyl , etc..
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248
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249
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250 =cut
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251
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252
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253
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254
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255
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256 =back
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257
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258
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259 =head1 SYNOPSIS
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260
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261
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262
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263 =head1 DESCRIPTION
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264
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265
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266
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267 =cut
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268