Mercurial > repos > konradpaszkiewicz > preppereadsforveletfasta

annotate shuffleSequences_fasta.pl @ 0:4d237a31970b default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author konradpaszkiewicz
date Tue, 07 Jun 2011 17:42:21 -0400
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4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #!/usr/bin/perl
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2
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3 if (!@ARGV) {
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4 print "Usage: $0 forward_reads.fa reverse_reaads.fa outfile.fa\n";
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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5 print "\tforward_reads.fa / reverse_reads.fa : paired reads to be merged\n";
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 print "\toutfile.fa : outfile to be created\n";
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7 system.exit(0);
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8 }
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9
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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10 $filenameA = $ARGV[0];
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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11 $filenameB = $ARGV[1];
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12 $filenameOut = $ARGV[2];
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13
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14 die "Could not open $filenameA" unless (-e $filenameA);
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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15 die "Could not open $filenameB" unless (-e $filenameB);
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17 open FILEA, "< $filenameA";
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18 open FILEB, "< $filenameB";
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4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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20 open OUTFILE, "> $filenameOut";
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4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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22 my ($lineA, $lineB);
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24 $lineA = <FILEA>;
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25 $lineB = <FILEB>;
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27 while(defined $lineA) {
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28 print OUTFILE $lineA;
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29 $lineA = <FILEA>;
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30 while (defined $lineA && $lineA !~ m/>/) {
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31 print OUTFILE $lineA;
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32 $lineA = <FILEA>;
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33 }
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35 print OUTFILE $lineB;
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36 $lineB = <FILEB>;
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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37 while (defined $lineB && $lineB !~ m/>/) {
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38 print OUTFILE $lineB;
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39 $lineB = <FILEB>;
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40 }
4d237a31970b Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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41 }