|
3
|
1 #!/usr/bin/perl
|
|
|
2
|
|
|
3 use strict;
|
|
|
4
|
|
|
5 my $indir = $ARGV[0];
|
|
|
6 my $matrix = $ARGV[1];
|
|
|
7 my $out = $ARGV[2];
|
|
|
8 my $strain_names = $ARGV[3];
|
|
|
9
|
|
|
10 my %strains_of_gb;
|
|
|
11 open(F,$strain_names);
|
|
|
12 while(<F>){
|
|
|
13 my $line = $_;
|
|
|
14 $line =~s/\n//g;$line =~s/\r//g;
|
|
|
15 my ($gb,$strain) = split(/\t/,$line);
|
|
|
16 $strains_of_gb{$gb} = $strain;
|
|
|
17 }
|
|
|
18 close(F);
|
|
|
19
|
|
|
20
|
|
|
21
|
|
|
22 my $cl_num = 0;
|
|
|
23 my $nb_strains = 1;
|
|
|
24 open(O,">$out");
|
|
|
25 open(U,">$out.upsetr.txt");
|
|
|
26 open(M,">$out.accessory_01matrix.txt");
|
|
|
27 open(F,$matrix);
|
|
|
28 my $firstline = <F>;
|
|
|
29 $firstline =~s/\n//g;$firstline =~s/\r//g;
|
|
|
30 my @infos = split(/\t/,$firstline);
|
|
|
31 print O "ClutserID";
|
|
|
32 print U "ClutserID";
|
|
|
33 print M "Gene";
|
|
|
34 for (my $j=1; $j <= $#infos; $j++){
|
|
|
35 my $gbfile = $infos[$j];
|
|
|
36 $gbfile =~s/\"//g;
|
|
|
37 $gbfile =~s/\.gb\.filt//g;
|
|
|
38 $gbfile =~s/\.gb\.rmdup//g;
|
|
|
39 my $strain = $strains_of_gb{$gbfile};
|
|
|
40 print O "\t".$strain;
|
|
|
41 print U "\t".$strain;
|
|
|
42 print M "\t".$strain;
|
|
|
43 $nb_strains++;
|
|
|
44 }
|
|
|
45 print O "\n";
|
|
|
46 print U "\n";
|
|
|
47 print M "\n";
|
|
|
48 while(<F>){
|
|
|
49 $cl_num++;
|
|
|
50 my @infos = split(/\t/,$_);
|
|
|
51 print O $cl_num;
|
|
|
52 print U $cl_num;
|
|
|
53 my $concat_accessory = "";
|
|
|
54 for (my $i = 1; $i <= $#infos; $i++){
|
|
|
55 my $val = $infos[$i];
|
|
|
56 $val =~s/\"//g;
|
|
|
57 $val =~s/\n//g;$val =~s/\r//g;
|
|
|
58 if ($val =~/\w+/){
|
|
|
59 print U "\t1";
|
|
|
60 $concat_accessory .= "\t1";
|
|
|
61 }
|
|
|
62 else{
|
|
|
63 print U "\t0";
|
|
|
64 $concat_accessory .= "\t0";
|
|
|
65 }
|
|
|
66 my @genes = split(/, /,$val);
|
|
|
67 my $concat = "";
|
|
|
68 foreach my $gene(@genes){
|
|
|
69 my $prot_id = $gene;
|
|
|
70 $concat .= "$prot_id,"
|
|
|
71 }
|
|
|
72 chop($concat);
|
|
|
73 if (scalar @genes == 0){
|
|
|
74 $concat = "-";
|
|
|
75 }
|
|
|
76 print O "\t".$concat;
|
|
|
77 }
|
|
|
78 if ($concat_accessory =~/0/){
|
|
|
79 print M $cl_num.$concat_accessory."\n";
|
|
|
80 }
|
|
|
81 print O "\n";
|
|
|
82 print U "\n";
|
|
|
83 }
|
|
|
84 close(F);
|
|
|
85 close(O);
|
|
|
86 close(U);
|
|
|
87 close(M);
|
