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comparison phyloconversion/change_sp.pl @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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-1:000000000000 0:5b9a38ec4a39
1 #!/usr/bin/perl -w
2 use strict;
3
4 my $infile = $ARGV[0];
5 my $changefile = $ARGV[1];
6 my $outfile = $ARGV[2];
7
8 open(IN, "$infile") or exit;
9 open(CHANGE, "$changefile");
10 open(OUT, ">$outfile") or exit;
11
12
13 my %speciesFor; #Hash to associate code with species name
14
15 while (<CHANGE>)
16 {
17 chomp;
18 my $currentinput = "$_";
19 if($currentinput =~m /\t/){ #must have a tab otherwise wrong file format
20 if($currentinput =~m /\t\t/){
21 print OUT "ERROR: file contains 2 tabs in a row. Check phytab format.\n";
22 die("ERROR: file contains 2 tabs in a row. Check it is in phytab format");
23 }else{
24 my @changepair = split(/\t/, $currentinput);
25 my $codename=$changepair[0];
26 my $sp_name = $changepair[1];
27 if (exists $speciesFor{$codename}) {
28 print OUT "ERROR: Species name specification for $codename is duplicated\n";
29 die("ERROR: Species name specifiation for for $codename is duplicated\n");
30 }else{
31 $speciesFor{$codename}=$sp_name;
32 }
33 }
34 }else{
35 die "ERROR: Species conversion table must be genefamily\tmodel and contain no blank lines\n";
36 }
37 }
38 while (<IN>) {
39 chomp;
40 my $currentinput = "$_";
41 if($currentinput =~m /\t/){ #must have a tab otherwise wrong file format
42 if($currentinput =~m /\t\t/){
43 print OUT "ERROR: file contains 2 tabs in a row. Check phytab format.\n";
44 die;
45 }else{
46 my @changepair = split(/\t/, $currentinput);
47 my $sp_name=$changepair[0];
48
49 if (exists $speciesFor{$sp_name}) {
50 $currentinput =~s /$sp_name/$speciesFor{$sp_name}/ ;
51 print OUT $currentinput."\n";
52 }else{
53 print OUT $currentinput."\n";
54 }
55 }
56 }else{
57 die "ERROR: Input a PHYTAB file in Tabular format\n";
58 }
59 }
60 close(IN);
61 close(OUT);
62 close(CHANGE);
63
64 sub change
65 {
66
67 my $changetext = shift;
68 $changetext =~ s/ /_/g;
69 return $changetext;
70 }