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1 #! /usr/bin/perl -w
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2
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3 use strict;
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4 use warnings;
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5
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6 # fastq_paired_reads_convention2.pl [input file] [left output file] [right output file]
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7
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8 die "Check arguments" unless @ARGV == 3;
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9
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10 #open (LEFT, '>data/left2.fastq') or die "Cannot create $ARGV[1]: $!\n";
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11 #open (RIGHT, '>data/right2.fastq') or die "Cannot create $ARGV[2]: $!\n";
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12 #open (INPUT, '<data/interlaced.fastq') or die "Cannot open $ARGV[0]: $!\n";
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13
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14 open (LEFT, '>', $ARGV[1]) or die "Cannot create $ARGV[1]: $!\n";
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15 open (RIGHT, '>', $ARGV[2]) or die "Cannot create $ARGV[2]: $!\n";
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16 open (INPUT, '<', $ARGV[0]) or die "Cannot open $ARGV[0]: $!\n";
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17
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18 my $which = 0;
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19 my $current_id;
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20
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21 while(<INPUT>) {
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22 chomp;
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23 if(/ 1\S*/){
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24 $_ =~ s/ 1\S*//;
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25 $_.='/1';
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26 $current_id = substr $_, 1;
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27 $which = 1;
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28 }
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29 if(/ 2\S*/){
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30 $_ =~ s/ 2\S*//;
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31 $_.='/2';
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32 $current_id = substr $_, 1;
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33 $which = 2;
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34 }
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35
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36 if($_ eq '+'){
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37 $_.=$current_id;
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38 }
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39
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40 if($which == 1){
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41 print LEFT "$_\n";
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42 }
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43 if($which == 2){
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44 print RIGHT "$_\n";
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45 }
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46 }
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47
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48 close (LEFT);
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49 close (RIGHT);
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50 close (INPUT); |
