[2] | 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 | my $command = ""; |
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| 6 | # a wrapper for paste for use in galaxy |
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| 7 | # pasteWrapper.pl [filename1] [filename2] [delimiter] [output] |
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| 8 | |
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| 9 | die "Check arguments" unless @ARGV == 4; |
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| 10 | |
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| 11 | if ($ARGV[2] eq 'T') { |
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| 12 | $command = "paste $ARGV[0] $ARGV[1]"; |
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| 13 | } elsif ($ARGV[2] eq 'C') { |
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| 14 | $command = "paste -d \",\" $ARGV[0] $ARGV[1]"; |
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| 15 | } elsif ($ARGV[2] eq 'D') { |
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| 16 | $command = "paste -d \"-\" $ARGV[0] $ARGV[1]"; |
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| 17 | } elsif ($ARGV[2] eq 'U') { |
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| 18 | $command = "paste -d \"_\" $ARGV[0] $ARGV[1]"; |
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| 19 | } elsif ($ARGV[2] eq 'P') { |
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| 20 | $command = "paste -d \"|\" $ARGV[0] $ARGV[1]"; |
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| 21 | } elsif ($ARGV[2] eq 'Dt') { |
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| 22 | $command = "paste -d \".\" $ARGV[0] $ARGV[1]"; |
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| 23 | } elsif ($ARGV[2] eq 'Sp') { |
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| 24 | $command = "paste -d \" \" $ARGV[0] $ARGV[1]"; |
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| 25 | } |
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| 26 | |
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| 27 | open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n"; |
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| 28 | open (PASTE, "$command |") or die "Cannot run paste:$!\n"; |
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| 29 | |
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| 30 | while (<PASTE>) { |
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| 31 | print OUT; |
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| 32 | } |
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| 33 | close OUT; |
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| 34 | close PASTE; |
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| 35 | |
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