Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/tnt2phytab.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
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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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 my $file = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 # read file with genes
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 open FILE, $file or die "ERROR: Cannot open file $file\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 my $firstline=0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 my $datatype;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 my $taxa;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 while (<FILE>) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $currentinput = "$_";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 if($firstline==0){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 if($currentinput =~ m/nstates/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 my @splitlines=split(' ',$currentinput);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 $splitlines[2] =~ s/\;//;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 if($splitlines[2] == 2){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 $datatype = "binary";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 }elsif($splitlines[2] > 2){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 $datatype = "multi";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 die "ERROR: file does not begin with nstates line. Must be TNT file exported from MorphoBank.org";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 if($firstline==1){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 if($currentinput =~ m/xread/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 die "ERROR: file does not contain xread line. Must be TNT file exported from MorphoBank.org";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 if($firstline==2){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 if($currentinput =~ m/Morpho/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 die "ERROR: file does not contain Morphobank Comment line. Must be TNT file exported from MorphoBank.org";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 if($firstline==3){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 if($currentinput =~ m/\d/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 my @splitlines=split(' ',$currentinput);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 $taxa = $splitlines[1]."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 die "ERROR: file does not contain number of taxa. Must be TNT file exported from MorphoBank.org";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 if($firstline==4){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 if($currentinput =~ m/\d/){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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49 die "ERROR: file does not contain empty line after taxa numbers . Must be TNT file exported from MorphoBank.org";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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50 }else{
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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51 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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52 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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53 if(($firstline>4)&&($firstline<(3+2+$taxa))){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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54 my @splitlines=split(' ',$currentinput);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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55 print $splitlines[0]."\t".$datatype."\t".$splitlines[0]."_".$datatype."\t".$splitlines[1]."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 $firstline++;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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58 }