Mercurial > repos > yufei-luo > s_mart

comparison SMART/bacteriaRegulatoryRegion_Detection/strictlyIncludeGff.pl @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/perl -w
2 ###
3 # But : protocol permettant la detection d'RNA non codant potentiel
4 #
5 # Entrees : fichier de mapping Smart gff3
6 # fichier gff des gènes
7 # fichier gff des clusters Cis regulateur potentiel
8 #
9 # Sortie : fichier gff des clusters ARN nc
10 #
11 ###------------------------------------------------------
12
13 use vars qw($USAGE);
14 use strict;
15
16 =head1 NAME
17
18 protocol_NC_V2_CTN3.pl
19
20 =head1 SYNOPSIS
21
22 % strictlyIncludeGff.pl -i toSelect.gff3 -t template.gff3 > result.gff3
23
24 =head1 DESCRIPTION
25
26 strictlyIncludeGff.pl - print elements strictly include in template (gff files)
27
28 -i|--input fileName gff input file name
29 -t|--template fileName gff template file name
30 [-h|--help] help mode then die
31
32 =head1 AUTHOR - CTN - mar.11
33 (from RNA-Vibrio/protocol_NC_V2_CTN3.pl - Claire KUCHLY)
34
35 =cut
36
37 #----------------------------------------------------------------------------
38 # check command line :
39 my $outFileName = "outSIG.gff3";
40 if ($#ARGV==0) {
41 die (exec("pod2text $0\n"));
42 } else {
43 foreach my $num (0 .. $#ARGV) {
44 SWITCH: for ($ARGV[$num]) {
45 /--input|-i/ && do { open(ARN,"<$ARGV[$num+1]")
46 or die "Error: Can't open \"$ARGV[$num+1]\", $!";
47 last };
48 /--template|-t/ && do { open(SEED,"<$ARGV[$num+1]")
49 or die "Error : Can't open file \"$ARGV[$num+1]\", $!";
50 last };
51 /--help|-h/ && do { exec("pod2text $0\n") ; die };
52 }
53 }
54 ##NC_011753.2 RefSeq gene 367 834 . - . locus_tag=VS_0001;db_xref=GeneID:7162789
55 # open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n";
56 my @seed ;
57 my $s=0;
58 while (my $seedLine = <SEED> ) {
59 my @list = split(/\t/,$seedLine);
60 $seed[$s][0]= $list[3] ; # position begin seed
61 $seed[$s][1]= $list[4] ; # position end seed
62 $seed[$s][2]= $list[6] ; # seed sens
63 $seed[$s][3]= $list[0] ; # chromesome name
64 $s++;
65 }
66 close SEED ;
67 while(my $ligne = <ARN>){
68 $s=0;
69 my @list = split(/\t/,$ligne);
70 while (($s <= $#seed)) {
71 if (($seed[$s][3] eq $list[0]) and ($seed[$s][0] <= $list[3]) and ($seed[$s][1] >= $list[4]) and ($seed[$s][2] eq $list[6])) { # if list include in seed + same direction
72 print "$ligne";
73 }
74 $s++;
75 }
76 }
77 close ARN ;
78 exit(0);
79 }