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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 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
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43 while (my $line=<IN>) {
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44 if ($line =~ /^#/) {
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45 #Ignore comment lines
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46 } else {
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47 chop($line);
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48 @in = split(/$del/, $line);
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49 foreach $field (@columns) {
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50 if (defined($in[$field-1])) {
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51 push(@out, $in[$field-1]);
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52 } else {
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53 push(@out, ".");
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54 }
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55 }
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56 print OUT join("\t",@out), "\n";
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57 @out = ();
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58 }
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59 }
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60
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61 #while (<IN>) {
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62 # chop;
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63 # @in = split /$del/;
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64 # foreach $field (@columns) {
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65 # if (defined($in[$field-1])) {
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66 # push(@out, $in[$field-1]);
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67 # } else {
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68 # push(@out, ".");
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69 # }
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70 # }
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71 # print OUT join("\t",@out), "\n";
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72 # @out = ();
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73 #}
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74 close IN;
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75
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76 close OUT;
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77
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