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comparison changeCase.pl @ 0:e6f966602870 draft

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Uploaded change_case tarball.
author devteam
date Tue, 04 Dec 2012 10:49:46 -0500
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-1:000000000000 0:e6f966602870
1 #! /usr/bin/perl -w
2
3 use strict;
4 use warnings;
5
6 my $columns = {};
7 my $del = "";
8 my @in = ();
9 my @out = ();
10 my $command = "";
11 my $field = 0;
12
13 # a wrapper for changing the case of columns from within galaxy
14 # isaChangeCase.pl [filename] [columns] [delim] [casing] [output]
15
16 die "Check arguments: $0 [filename] [columns] [delim] [casing] [output]\n" unless @ARGV == 5;
17
18 # process column input
19 $ARGV[1] =~ s/\s+//g;
20 foreach ( split /,/, $ARGV[1] ) {
21 if (m/^c\d{1,}$/i) {
22 s/c//ig;
23 $columns->{$_} = --$_;
24 }
25 }
26
27 die "No columns specified, columns are not preceeded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0;
28
29 my $column_delimiters_href = {
30 'TAB' => q{\t},
31 'COMMA' => ",",
32 'DASH' => "-",
33 'UNDERSCORE' => "_",
34 'PIPE' => q{\|},
35 'DOT' => q{\.},
36 'SPACE' => q{\s+}
37 };
38
39 $del = $column_delimiters_href->{$ARGV[2]};
40
41 open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n";
42 open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
43 while (<IN>) {
44 chop;
45 @in = split /$del/;
46 for ( my $i = 0; $i <= $#in; ++$i) {
47 if (exists $columns->{$i}) {
48 push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i]));
49 } else {
50 push(@out, $in[$i]);
51 }
52 }
53 print OUT join("\t",@out), "\n";
54 @out = ();
55 }
56 close IN;
57
58 close OUT;