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annotate libs/sratoolkit.2.8.0-centos_linux64/example/perl/simplefastq.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 #
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6 # this script has to be fed from vdb-dump
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7 # it takes input on STDIN
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8 # the input has to be a stream of lines
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9 # each line containing "SPOT_ID,NAME,SPOT_LEN,READ,QUALITY" delimited by tab
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10 #
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11 # example:
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12 #
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13 # vdb-dump SRR000001 -C "SPOT_ID,NAME,SPOT_LEN,READ,(INSDC:quality:text:phred_33)QUALITY" -f tab | simplefastq.pl SRR000001 > SRR000001.fastq
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14 #
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15
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16 my $line;
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17 my $base = $ARGV[ 0 ];
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18
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19 if ( !defined ( $base ) )
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20 {
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21 $base = "out";
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22 }
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23
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24 while ( defined ( $line = <STDIN> ) )
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25 {
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26 #remove line-feeds, white space etc.
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27 chomp( $line );
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28 @tokens = split( /\s/, $line );
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29
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30 print( '@' );
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31 print( "$base.$tokens[0] $tokens[1] length=$tokens[2]\n" );
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32 print( "$tokens[3]\n" );
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33 print( "+$base.$tokens[0] $tokens[1] length=$tokens[2]\n" );
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34 print( "$tokens[4]\n" );
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35 }