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comparison phyloconversion/beautify_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
3 use strict;
4
5 use FindBin;
6 use lib "$FindBin::Bin/lib";
7 use Bio::DB::Fasta;
8 use Bio::SeqIO;
9 use Bio::Seq;
10
11 #inputs
12 my $infile=shift(@ARGV);
13 my $outfile=shift(@ARGV);
14 my $delpipes=shift(@ARGV);
15 my $convgi=shift(@ARGV);
16 my $delslash=shift(@ARGV);
17 my $renumber=shift(@ARGV);
18 my $space=shift(@ARGV);
19
20 my $seqid;
21 my $newnumbers=1; #for sequential renumbering of header
22 # open infile fasta file
23 my $in_obj = Bio::SeqIO->new(-file => $infile, '-format' =>'fasta');
24 open FILE, ">$outfile" or die $!;
25
26 while (my $seq = $in_obj->next_seq() ) {
27 my $sequence = $seq->seq;
28 $seqid = $seq->id;
29
30 if($delslash eq 'yes'){
31 $seqid =~ s/\\/_/g;
32 }
33 if($convgi eq 'yes'){
34 $seqid =~ s/gi\|/gi_/g;
35 }
36 if($delpipes eq 'yes'){
37 $seqid =~ s/\|/ /g;
38 }
39 $sequence =~ s/\n//g;
40 $sequence =~ tr/a-z/A-Z/;
41 print FILE ">";
42 if($renumber eq 'yes'){
43 print FILE $newnumbers;
44 if($space eq 'yes'){
45 print FILE " ";
46 }
47 $newnumbers++;
48 }
49 print FILE $seqid." ".$seq->desc."\n".$sequence."\n";
50 }