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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 changing the case of columns from within galaxy
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14 # isaChangeCase.pl [filename] [columns] [delim] [casing] [output]
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15
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16 die "Check arguments: $0 [filename] [columns] [delim] [casing] [output]\n" unless @ARGV == 5;
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17
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18 # process column input
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19 $ARGV[1] =~ s/\s+//g;
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20 foreach ( split /,/, $ARGV[1] ) {
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21 if (m/^c\d{1,}$/i) {
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22 s/c//ig;
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23 $columns->{$_} = --$_;
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24 }
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25 }
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26
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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;
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28
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29 my $column_delimiters_href = {
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30 'TAB' => q{\t},
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31 'COMMA' => ",",
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32 'DASH' => "-",
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33 'UNDERSCORE' => "_",
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34 'PIPE' => q{\|},
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35 'DOT' => q{\.},
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36 'SPACE' => q{\s+}
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37 };
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38
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39 $del = $column_delimiters_href->{$ARGV[2]};
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40
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41 open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n";
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42 open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
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43 while (<IN>) {
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44 chop;
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45 @in = split /$del/;
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46 for ( my $i = 0; $i <= $#in; ++$i) {
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47 if (exists $columns->{$i}) {
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48 push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i]));
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49 } else {
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50 push(@out, $in[$i]);
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51 }
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52 }
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53 print OUT join("\t",@out), "\n";
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54 @out = ();
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55 }
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56 close IN;
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57
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58 close OUT;
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