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annotate libs/sratoolkit.2.8.0-centos_linux64/example/perl/splitfastq.pl @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/perl -w
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2
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3 use IO::File;
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4
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5 my $line;
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6 my $state = 0;
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7 my %filehandles;
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8 my $current_filehandle;
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9 my $base = $ARGV[ 0 ];
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10
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11 if ( !defined ( $base ) )
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12 {
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13 $base = "out";
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14 }
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15
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16 while ( defined ( $line = <STDIN> ) )
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17 {
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18 #remove line-feeds, white space etc.
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19 chomp( $line );
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20
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21 if ( $state == 0 )
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22 {
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23 # get the first word
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24 my $word0 = ( split( /\s+/, $line ) )[ 0 ];
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25
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26 # start with the beginning of the word, until '/' found, continue with numbers to end of string
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27 if ( $word0 =~ /^[^\/]+\/(\d+)$/ )
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28 {
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29 # grep what matched after the '/'
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30 my $selector = $1;
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31 if ( !defined ( $filehandles{$selector}) )
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32 {
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33 $filehandles{$selector} = new IO::File( "$base.$selector.fastq", "w" );
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34 }
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35 $current_filehandle = $filehandles{$selector};
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36 }
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37 }
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38
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39 if ( defined( $current_filehandle ) )
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40 {
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41 $current_filehandle -> print( "$line\n" );
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42 }
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43
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44 $state ++;
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45 $state &= 0x3;
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46 }