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comparison SMART/bacteriaRegulatoryRegion_Detection/sortGff.pl @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 #!/usr/bin/perl -w
2 ###
3 # But : ajout ou modif de couleur d'un gff
4 #
5 # Entrees : fichier gff
6 #
7 # Sortie : gff affiche a l'ecran
8 #
9 ###------------------------------------------------------
10
11 #!/usr/bin/perl -w
12
13 use vars qw($USAGE);
14 use strict;
15
16 =head1 NAME
17
18 sortGff.pl - sort a gff file
19
20 =head1 SYNOPSIS
21
22 % sortGff.pl -i file.gff [-h]
23
24 =head1 DESCRIPTION
25 This script will sort a gff file (only when inversion of two successive lines).
26
27 -i|--input fileName gff input file name
28 -o|--output fileName gff3 output file name
29 [-h|--help] help mode then die
30
31 =head1 AUTHOR - Claire Toffano-Nioche - mar.11
32
33 =cut
34
35 #-----------------------
36 my ($fileName, $colourGff, $outFileName) = ("", "", "sortOut.gff3") ;
37 # command line check
38 foreach my $num (0 .. $#ARGV) {
39 SWITCH: for ($ARGV[$num]) {
40 /--input|-i/ && do {
41 $fileName=$ARGV[$num+1];
42 open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ;
43 last };
44 # /--output|-o/ && do {
45 # $outFileName=$ARGV[$num+1];
46 # last };
47 /--help|-h/ && do { exec("pod2text $0\n") ; die };
48 }
49 }
50 # informations retrieval
51 # open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n";
52 my @lines = <fichierGff> ;
53 close fichierGff ;
54 # treatment
55 #print "gff file read ; number of lines : $#lines\n";
56 my $previous = 0;
57 my $i = 0;
58 #print "$#lines\n" ;
59 while ($i <= $#lines) {
60 my @infos = split('\t', $lines[$i]) ;
61 #print "info[3]:$infos[3]; prv:$previous!\n";
62 if ($infos[3] < $previous) {
63 &exchange($i, $infos[3]) ;
64 $previous=$infos[3] ;
65 $i--;
66 }
67 $previous=$infos[3];
68 $i++;
69 }
70 for (my $i=0 ; $i <= $#lines ; $i++) {
71 # print OUT $lines[$i] ;
72 print $lines[$i] ;
73 }
74 #close OUT ;
75 exit(0);
76 #-----------------------
77 sub exchange {
78 my ($index, $position) = @_ ;
79 my @info_col = split("\t", $lines[$index-1]) ;
80 if ($info_col[3] > $position) {
81 #print "$lines[$index]";
82 my $line_to_push = $lines[$index-1] ;
83 $lines[$index-1] = $lines[$index] ;
84 $lines[$index] = $line_to_push ;
85 } else {
86 print "TODO : push > one line\n" ;
87 }
88 }