Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/length_outliers.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:
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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 Bio::DB::Fasta;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 use Bio::SeqIO;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 use Bio::Seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 #inputs
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 my $infile=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 my $outfile=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 my $deloutfile=shift(@ARGV);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $percent=shift(@ARGV);
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14
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 my $seqid;
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16 my $newnumbers=1; #for sequential renumbering of header
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17
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 open FILE, ">$outfile" or die $!;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 open DELFILE, ">$deloutfile" or die $!;
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20
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21
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 # open infile fasta file to get average length
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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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24
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 my $seqcount;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 my $seqsum = 0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 my $avelen;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 while (my $seq = $in_obj->next_seq() ) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 my $sequence = $seq->seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 my $seqlen = length($sequence);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 $seqcount++;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 $seqsum = $seqsum + $seqlen;
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33 }
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34 $avelen = $seqsum/$seqcount;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 print "AVE= $avelen \n";
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36
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37
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 # open infile fasta file to get average length
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 $in_obj = Bio::SeqIO->new(-file => $infile, '-format' =>'fasta');
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 while (my $seq = $in_obj->next_seq() ) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 my $sequence = $seq->seq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 $seqid = $seq->id;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 $sequence =~ s/\n//g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 $sequence =~ tr/a-z/A-Z/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 my $seqlen = length($sequence);
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47
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 if($seqlen > ($avelen * ($percent/100) ) ){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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49 print FILE ">";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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50 print FILE $seqid." ".$seq->desc."\n".$sequence."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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51 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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52 print "Writing sequence of $seqlen to DELFILE\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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53 print DELFILE ">";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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54 print DELFILE $seqid." ".$seq->desc."\n".$sequence."\n";
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55 }
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56 }
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57
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58 close FILE;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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59 close DELFILE;