[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 | |
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| 6 | my @columns = (); |
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| 7 | my $del = ""; |
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| 8 | my @in = (); |
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| 9 | my @out = (); |
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| 10 | my $command = ""; |
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| 11 | my $field = 0; |
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| 12 | |
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| 13 | # a wrapper for cut for use in galaxy |
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| 14 | # cutWrapper.pl [filename] [columns] [delim] [output] |
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| 15 | |
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| 16 | die "Check arguments\n" unless @ARGV == 4; |
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| 17 | |
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| 18 | $ARGV[1] =~ s/\s+//g; |
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| 19 | foreach ( split /,/, $ARGV[1] ) { |
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| 20 | if (m/^c\d{1,}$/i) { |
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| 21 | push (@columns, $_); |
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| 22 | $columns[@columns-1] =~s/c//ig; |
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| 23 | } |
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| 24 | } |
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| 25 | |
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| 26 | die "No columns specified, columns are not preceded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if @columns == 0; |
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| 27 | |
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| 28 | my $column_delimiters_href = { |
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| 29 | 'T' => q{\t}, |
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| 30 | 'C' => ",", |
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| 31 | 'D' => "-", |
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| 32 | 'U' => "_", |
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| 33 | 'P' => q{\|}, |
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| 34 | 'Dt' => q{\.}, |
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| 35 | 'Sp' => q{\s+} |
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| 36 | }; |
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| 37 | |
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| 38 | $del = $column_delimiters_href->{$ARGV[2]}; |
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| 39 | |
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| 40 | open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n"; |
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| 41 | open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n"; |
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| 42 | while (<IN>) { |
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| 43 | chop; |
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| 44 | @in = split /$del/; |
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| 45 | foreach $field (@columns) { |
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| 46 | if (defined($in[$field-1])) { |
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| 47 | push(@out, $in[$field-1]); |
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| 48 | } else { |
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| 49 | push(@out, "."); |
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| 50 | } |
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| 51 | } |
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| 52 | print OUT join("\t",@out), "\n"; |
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| 53 | @out = (); |
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| 54 | } |
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| 55 | close IN; |
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| 56 | |
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| 57 | close OUT; |
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| 58 | |
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