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comparison rapsodyn/listfiltering.pl @ 8:d857538d9fea draft

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author mcharles
date Fri, 10 Oct 2014 07:05:36 -0400
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7:3f7b0788a1c4 8:d857538d9fea
1 #!/usr/bin/perl
2 # v1.0.1 added log, and two different type of filtering (common / specific)
3 use strict;
4 use Getopt::Long;
5
6 my $list1_file;
7 my $list2_file;
8 my $log_file;
9 my $NB_COL=1;
10 my $TYPE = "common";
11 my %header;
12 my $nb_list1 = 0;
13 my $nb_list2 = 0;
14 my $nb_common = 0;
15
16
17 GetOptions (
18 "list1_file=s" => \$list1_file,
19 "list2_file=s" => \$list2_file,
20 "log_file=s" => \$log_file,
21 "type=s" => \$TYPE,
22 "nb_col=i" => \$NB_COL
23 ) or die("Error in command line arguments\n");
24
25 open(L2, $list2_file) or die("Can't open $list2_file\n");
26 while (my $line=<L2>){
27 $nb_list2++;
28 chomp($line);
29 my @fields = split(/\s+/,$line);
30 my $ref="";
31 my $compt=0;
32 while ($compt<$NB_COL){
33 if ($ref){$ref.="\t";}
34 $ref.=$fields[$compt];
35 $compt++;
36 }
37 $header{$ref}=$line;
38 }
39 close (L2);
40
41
42 open(L1, $list1_file) or die("Can't open $list1_file\n");
43 while (my $line=<L1>){
44 $nb_list1++;
45 my @fields = split(/\s+/,$line);
46 my $ref="";
47 my $compt=0;
48 while ($compt<$NB_COL){
49 if ($ref){$ref.="\t";}
50 $ref.=$fields[$compt];
51 $compt++;
52 }
53 # my $ref = "$fields[0]\t$fields[1]";
54
55 if ($header{$ref}){
56 $nb_common++;
57 if ($TYPE eq "common"){
58 print $line;
59 }
60 elsif ($TYPE eq "specific") {
61 }
62 else {
63 }
64 }
65 else {
66 if ($TYPE eq "common"){
67 }
68 elsif ($TYPE eq "specific") {
69 print $line;
70 }
71 else {
72 }
73 }
74
75 }
76 my $nb_list1_only = $nb_list1 - $nb_common;
77 my $nb_list2_only = $nb_list2 - $nb_common;
78
79 close(L1);
80 open (LF,">$log_file") or die("Can't open $log_file\n");
81 print LF "\n####\t List Filtering \n";
82 print LF "#List 1 :\t$nb_list1 ($nb_list1_only)\n";
83 print LF "#List 2 :\t$nb_list2 ($nb_list2_only)\n";
84 print LF "#Common :\t$nb_common\n";
85 close (LF);
86