Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phyloconversion/remove_gbs_dupes.pl @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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-1:000000000000 | 0:5b9a38ec4a39 |
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1 #!/usr/bin/perl -w | |
2 use strict; | |
3 | |
4 my $datafile = $ARGV[0]; | |
5 my $keepfile = $ARGV[1]; | |
6 my $delfile = $ARGV[2]; | |
7 my $subsp = $ARGV[3]; | |
8 my $var = $ARGV[4]; | |
9 | |
10 open (FILE,"<$datafile") or die "Cannot open file input file\n"; | |
11 open (KFILE,">$keepfile") or die "Cannot open file $keepfile\n"; | |
12 open (DFILE,">$delfile") or die "Cannot open file delfile\n"; | |
13 | |
14 my $keep = 1; | |
15 | |
16 while (<FILE>) | |
17 { | |
18 if($_ =~ m/_\d/){ | |
19 $keep=0; | |
20 }else{ | |
21 if($subsp==1){ | |
22 if($_ =~ m/subsp/){ | |
23 $keep=0; | |
24 } | |
25 } | |
26 if($var==1){ | |
27 if($_ =~ m/_var_/){ | |
28 $keep=0; | |
29 } | |
30 } | |
31 } | |
32 | |
33 if($keep == 0){ | |
34 print DFILE $_; | |
35 }else{ | |
36 print KFILE $_; | |
37 } | |
38 $keep=1; #reset variable. Default is keep | |
39 } | |
40 close FILE; | |
41 close KFILE; | |
42 close DFILE; | |
43 |