|
3
|
1 #!/usr/bin/perl
|
|
|
2
|
|
|
3 use strict;
|
|
|
4
|
|
|
5 my $chrom_focus = $ARGV[0];
|
|
|
6
|
|
|
7 for (my $i=37; $i >= 1; $i--){print "NL$i;";}exit;
|
|
|
8
|
|
|
9 print "[\n";
|
|
|
10 my %gene_positions;
|
|
|
11 open(G,"Map_annotation_ID_NFGwada.gff3.gff3");
|
|
|
12 while(<G>){
|
|
|
13 my $line = $_;
|
|
|
14 $line =~s/\n//g;$line =~s/\r//g;
|
|
|
15 my @infos = split("\t",$line);
|
|
|
16 if ($infos[2] eq "mRNA" && /ID=([^;]+);/){
|
|
|
17 my $gene = $1;
|
|
|
18 my $start = $infos[3];
|
|
|
19 my $end = $infos[4];
|
|
|
20 my $chr = $infos[0];
|
|
|
21 #if ($chrom_focus && $chrom_focus ne $chr){next;}
|
|
|
22 $gene_positions{$gene} = "$chr-$start-$end";
|
|
|
23 }
|
|
|
24 }
|
|
|
25 close(G);
|
|
|
26
|
|
|
27 open(G,"Map_annotation_ID_NLova7.gff3.gff3");
|
|
|
28 while(<G>){
|
|
|
29 my $line = $_;
|
|
|
30 $line =~s/\n//g;$line =~s/\r//g;
|
|
|
31 my @infos = split("\t",$line);
|
|
|
32 if ($infos[2] eq "mRNA" && /ID=([^;]+);/){
|
|
|
33 my $gene = $1;
|
|
|
34 my $start = $infos[3];
|
|
|
35 my $end = $infos[4];
|
|
|
36 my $chr = $infos[0];
|
|
|
37 #if ($chrom_focus && $chrom_focus ne $chr){next;}
|
|
|
38 $gene_positions{$gene} = "$chr-$start-$end";
|
|
|
39 }
|
|
|
40 }
|
|
|
41 close(G);
|
|
|
42
|
|
|
43 my $lines = "";
|
|
|
44 open(F,"orthofinder_matrix.txt");
|
|
|
45 <F>;
|
|
|
46 while(<F>){
|
|
|
47 my $line = $_;
|
|
|
48 $line =~s/\n//g;$line =~s/\r//g;
|
|
|
49 my @infos = split("\t",$line);
|
|
|
50 my $nb_found = 0;
|
|
|
51 my $index = 0;
|
|
|
52 for (my $i = 1; $i <= $#infos; $i++){
|
|
|
53 my $val = $infos[$i];
|
|
|
54 if ($val =~/\w+/){
|
|
|
55 $nb_found++;
|
|
|
56 $index = $i;
|
|
|
57 }
|
|
|
58 }
|
|
|
59 if ($nb_found == 1){
|
|
|
60 #print "$index\n";
|
|
|
61 }
|
|
|
62 #next;
|
|
|
63 if ($nb_found == $#infos){
|
|
|
64 my $gene1 = $infos[1];
|
|
|
65 my $gene2 = $infos[7];
|
|
|
66 if ($gene1 !~/,/ && $gene2 !~/,/){
|
|
|
67 my ($chr1,$start1,$end1) = split(/-/,$gene_positions{$gene1});
|
|
|
68 my ($chr2,$start2,$end2) = split(/-/,$gene_positions{$gene2});
|
|
|
69 $chr2 = lc($chr2);
|
|
|
70 #if ($chr1 eq $chr2 && $chr1 eq "$chrom_focus"){
|
|
|
71 if ($chr1 ne $chr2 && $chr2 =~/\w+/){
|
|
|
72 #if ($chr1 eq $chr2){
|
|
|
73 if ($chr1=~/chr(\d+)/){
|
|
|
74 #my $nb = $1 * 1400000;
|
|
|
75 my $nb = 0;
|
|
|
76 $start1 += $nb;
|
|
|
77 $end1 += $nb;
|
|
|
78 }
|
|
|
79 if ($chr2=~/chr(\d+)/){
|
|
|
80 #my $nb = $1 * 1400000;
|
|
|
81 my $nb = 0;
|
|
|
82 $start2 += $nb;
|
|
|
83 $end2 += $nb;
|
|
|
84 }
|
|
|
85 #[{"name": "574556.4.fasta","start": 717247,"end": 718620,"strand": "-","lcb_idx": 1},
|
|
|
86 #$lines .= "[{\"name\": \"1.fasta\",\"start\": $start1,\"end\": $end1,\"strand\": \"-\",\"lcb_idx\": 1},{\"name\": \"2.fasta\",\"start\": $start2,\"end\": $end2,\"strand\": \"-\",\"lcb_idx\": 2}],\n";
|
|
|
87 $chr1 =~s/chr/NF/g;
|
|
|
88 $chr2 =~s/chr/NL/g;
|
|
|
89 print "$chr1 $start1 $end1 $chr2 $start2 $end2\n";
|
|
|
90 }
|
|
|
91 }
|
|
|
92 }
|
|
|
93 }
|
|
|
94 close(F);
|
|
|
95
|
|
|
96 chop($lines);
|
|
|
97 chop($lines);
|
|
|
98 #print "$lines\n]";
|
