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comparison phyloconversion/raxify_fasta.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 $outfile = $ARGV[1];
6
7 open(IN, "$infile") or exit;
8 open(OUT, ">$outfile") or exit;
9
10 while (<IN>) {
11 my $line = $_;
12 if($line =~ m/\>/ ){
13 $line=raxify($line);
14 }
15 if($line =~ m/\n/){
16 print OUT $line;
17 }else{
18 print OUT $line."\n";
19 }
20 }
21 close(IN);
22 close(OUT);
23
24 sub raxify
25 {
26 my $raxline = shift;
27 $raxline = substr($raxline,0,51);
28 $raxline =~ s/\./_/g;
29 $raxline =~ s/\|/_/g;
30 $raxline =~ s/ /_/g;
31 return $raxline;
32 }