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18
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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
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11 #!/usr/bin/perl -w
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12
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13 use vars qw($USAGE);
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14 use strict;
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15
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16 =head1 NAME
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17
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18 sortGff.pl - sort a gff file
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19
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20 =head1 SYNOPSIS
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21
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22 % sortGff.pl -i file.gff [-h]
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23
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24 =head1 DESCRIPTION
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25 This script will sort a gff file (only when inversion of two successive lines).
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26
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27 -i|--input fileName gff input file name
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28 -o|--output fileName gff3 output file name
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29 [-h|--help] help mode then die
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30
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31 =head1 AUTHOR - Claire Toffano-Nioche - mar.11
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32
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33 =cut
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34
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35 #-----------------------
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36 my ($fileName, $colourGff, $outFileName) = ("", "", "sortOut.gff3") ;
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37 # command line check
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38 foreach my $num (0 .. $#ARGV) {
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39 SWITCH: for ($ARGV[$num]) {
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40 /--input|-i/ && do {
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41 $fileName=$ARGV[$num+1];
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42 open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ;
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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 $0\n") ; die };
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48 }
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49 }
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50 # informations retrieval
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51 # open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n";
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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 my $previous = 0;
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57 my $i = 0;
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58 #print "$#lines\n" ;
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59 while ($i <= $#lines) {
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60 my @infos = split('\t', $lines[$i]) ;
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61 #print "info[3]:$infos[3]; prv:$previous!\n";
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62 if ($infos[3] < $previous) {
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63 &exchange($i, $infos[3]) ;
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64 $previous=$infos[3] ;
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65 $i--;
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66 }
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67 $previous=$infos[3];
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68 $i++;
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69 }
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70 for (my $i=0 ; $i <= $#lines ; $i++) {
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71 # print OUT $lines[$i] ;
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72 print $lines[$i] ;
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73 }
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74 #close OUT ;
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75 exit(0);
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76 #-----------------------
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77 sub exchange {
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78 my ($index, $position) = @_ ;
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79 my @info_col = split("\t", $lines[$index-1]) ;
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80 if ($info_col[3] > $position) {
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81 #print "$lines[$index]";
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82 my $line_to_push = $lines[$index-1] ;
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83 $lines[$index-1] = $lines[$index] ;
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84 $lines[$index] = $line_to_push ;
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85 } else {
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86 print "TODO : push > one line\n" ;
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87 }
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88 }
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