Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/beautify_fasta.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl -w
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 use FindBin;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 use lib "$FindBin::Bin/lib";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 use Bio::DB::Fasta;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 use Bio::SeqIO;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 use Bio::Seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 #inputs
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 my $infile=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $outfile=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 my $delpipes=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 my $convgi=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 my $delslash=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 my $renumber=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 my $space=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 my $seqid;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 my $newnumbers=1; #for sequential renumbering of header
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 # open infile fasta file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 my $in_obj = Bio::SeqIO->new(-file => $infile, '-format' =>'fasta');
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 open FILE, ">$outfile" or die $!;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 while (my $seq = $in_obj->next_seq() ) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 my $sequence = $seq->seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 $seqid = $seq->id;
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29
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 if($delslash eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 $seqid =~ s/\\/_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 if($convgi eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 $seqid =~ s/gi\|/gi_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 if($delpipes eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 $seqid =~ s/\|/ /g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 $sequence =~ s/\n//g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 $sequence =~ tr/a-z/A-Z/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 print FILE ">";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 if($renumber eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 print FILE $newnumbers;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 if($space eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 print FILE " ";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 $newnumbers++;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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49 print FILE $seqid." ".$seq->desc."\n".$sequence."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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50 }