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annotate phylogenies/genetree_read_placement.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 use warnings;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 ##For debugging command line pass, uncomment next
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 #for (my $i=0; $i < @ARGV; $i++){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 # print "Parameter #$i ".$ARGV[$i]."\n\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 #}
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 #exit;
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11
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 my $newgenes=shift(@ARGV); #0 new genes to align
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $align = shift(@ARGV); #1 alignment program to use
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 my $path = shift(@ARGV); #2 path to tree and gene data
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 my $name = shift(@ARGV); #3 name of gene family
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16
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 #If $newgenes has not hits, do not do read placement, just write tree with no hits
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 my $buffer;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 my $lines = 0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 open(FILE, $newgenes) or die "Can't open `$newgenes': $!";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 while (sysread FILE, $buffer, 4096) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 $lines += ($buffer =~ tr/\n//);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 close FILE;
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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 if($lines < 1){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 print "No hits found. Skipping read placement\n Tree copied to output.\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 system "cp $path.tre RAxML_labelledTree.EPA_TEST";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 system "cp $path.tre RAxML_originalLabelledTree.EPA_TEST";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 }else{
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31
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 #First concatenate fasta files and align
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 system "cat $newgenes $path.fas > toalign.fas";
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34
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 if($align eq "MUSCLE"){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 system "muscle -in toalign.fas -out aligned.fas";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 elsif($align eq "MAFFT") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 system "mafft --auto toalign.fas > aligned.fas";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 elsif($align eq "PRANK") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 system "prank -d=toalign.fas -o=aligned -f=fasta -F";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 system "mv aligned.2.fas aligned.fas";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 #convert to phylip format, uses seqConverter.pl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 system "/home/galaxy/galaxy-dist/tools/oakley_dev/seqConverterG.pl -daligned.fas -ope -Oaligned.phy";
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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 system "raxmlHPC-PTHREADS-SSE3 -f v -s aligned.phy -m PROTGAMMAWAG -t $path.tre -n EPA_TEST -T 4";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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50 }
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51
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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52 #Now make tab delimited file to use in tab2trees
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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53 #open treefile to read tree line
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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54 open(TREE, "<","RAxML_labelledTree.EPA_TEST") or die "Can't open RESULT File!";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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55 my $finaltree;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 while (<TREE>){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 if($_ =~ /\;/m){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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58 $finaltree = $_;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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59 chomp($finaltree);
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60 }
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61 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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62 close TREE;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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63
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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64 $name =~ s/ /_/g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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65 chomp($name);
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66 #remove clade labels
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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67 $finaltree =~ s/\[I\d+\]//g;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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68 open(TAB, '>treeout.tab') or die "Can't open File!";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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69 print TAB $name."\t".$finaltree."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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70 close TAB;