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1 #!/usr/bin/perl -w
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2 ###
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3 # But : ajout ou modif de couleur d'un gff
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4 #
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5 # Entrees : fichier gff
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6 #
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7 # Sortie : gff affiche a l'ecran
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8 #
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9 ###------------------------------------------------------
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10 use vars qw($USAGE);
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11 use strict;
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12
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13 =head1 NAME
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14
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15 colorGff.pl - add or change color of a gff file
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16
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17 =head1 SYNOPSIS
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18
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19 % colorGff.pl -i file.gff -c color [-h]
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20
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21 =head1 DESCRIPTION
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22 This script will parse DOOR repport file and write information in gff3 format.
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23
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24 -i|--input fileName gff input file name
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25 -c|--color RGBcode RGB code for color
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26 -o|--output fileName gff3 output file name
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27 [-h|--help] help mode then die
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28
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29 =head1 AUTHOR - Claire Toffano-Nioche - jan.11
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30
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31 =cut
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32 #-----------------------
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33 my ($fileName, $colourGff, $outFileName) = ("", "", "colorOut.gff3") ;
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34 # command line check
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35 foreach my $num (0 .. $#ARGV) {
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36 SWITCH: for ($ARGV[$num]) {
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37 /--input|-i/ && do {
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38 $fileName=$ARGV[$num+1];
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39 open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ;
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40 last };
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41 /--color|-c/ && do {
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42 $colourGff =$ARGV[$num+1]." ".$ARGV[$num+2]." ".$ARGV[$num+3];
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43 last };
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44 # /--output|-o/ && do {
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45 # $outFileName=$ARGV[$num+1];
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46 # last };
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47 /--help|-h/ && do { exec("pod2text $0\n") ; die };
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48 }
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49 }
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50 # open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n";
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51 # informations retrieval
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52 my @lines = <fichierGff> ;
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53 close fichierGff ;
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54 # treatment
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55 #print "gff file read ; number of lines : $#lines\n";
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56 for (my $i=0 ; $i <= $#lines ; $i++) {
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57 if ($lines[$i] =~ /;/) {
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58 if ($lines[$i] =~ /color=/) {
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59 $lines[$i] =~ s/color=.*;/color=$colourGff;/ ;
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60 } else { # add colour
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61 $lines[$i] =~ s/;/;color=$colourGff;/ ;
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62 }
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63 } else { # (no = gff bug if col9 begin with semi-coma ?) or only one tag : add color tag
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64 chomp($lines[$i]) ;
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65 $lines[$i] .= "; color=".$colourGff.";\n";
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66 }
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67 # print OUT $lines[$i] ;
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68 print $lines[$i];
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69 }
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70 # close OUT ;
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71 exit(0);
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