Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/phylocatenator.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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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 use warnings;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 #phylocatenator.pl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 #Written by Todd H. Oakley UCSB
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7 #Version 1.0 May, 2012
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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 #phyloconcatenator.pl [infile] [also requires arguments 1-8 detailed below]
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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 #Version 1.0.1 Sept 2012 -- fixed a bug that led sometimes to species with no data being retained.
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12 #This bug would not affect the data that was retained, so if raxml ran all was fine. However,
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 #raxml will not run with species that have completely missing data. Added extra section to remove
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 #those species.
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15
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 #For debugging command line pass, uncomment next
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 #for(my $i=0; $i < @ARGV; $i++){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 # print "Arg $i: $ARGV[$i] \n\n";
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19 #}
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 #exit;
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21
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22 die "Check arguments" unless @ARGV == 9;
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23
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24 #Obtain Arguments
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25 my $infile1=shift(@ARGV); #0 input file
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26 my $mingf_persp=shift(@ARGV); #1 minimum number of genefamiles to keep species
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27 my $minsp_pergf=shift(@ARGV); #2 minimum number of species to keep genefamily
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28 my $min_gf_len =shift(@ARGV); #3 minimum gene family length
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29 my $speciesfile=shift(@ARGV); #4 optional species file 'None' if false
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30 my $modelsfile=shift(@ARGV); #5 models file
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31 my $outfile=shift(@ARGV); #6 data outfile
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32 my $partfile=shift(@ARGV); #7 partition file
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33 my $htmlfile=shift(@ARGV); #8 html file
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34
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35 #Open 2 output files
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36 open (OUT, ">$outfile") or die "Cannot create $outfile \n";
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37 open (PART, ">$partfile") or die "Cannot create $partfile\n";
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38 open (TABLE, ">$htmlfile") or die "Cannot create $htmlfile\n";
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39
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40 my %HoAdatatable;
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41 my %HoGF;
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42 my %lengthof;
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43 my %ModelFor;
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44 my $line = "";
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45
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46 my @specieslist;
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47 my @genelist;
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48 my @nsp;
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49 my $nsl=1;
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50 my @uniquemodels;
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51 my @nullmodels;
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52 my @retainedspecies;
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53
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54 # read file with species
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55 unless($speciesfile eq 'None'){
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56 open SPFILE, $speciesfile or die "ERROR: Cannot open file $speciesfile\n\n";
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57 $nsl=0;
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58 while (<SPFILE>) {
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59 chomp;
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60 my $currentinput = "$_";
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61 if($currentinput =~m /\w/){ #must have a word otherwise empty
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62 push(@nsp, $currentinput);
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63 }else{
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64 die "ERROR: Fewer than 4 species meet your specified criteria.\n";
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65 }
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66 # if(@nsp < 4){
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67 # die "ERROR: Species file must have more than 4 species.\n";
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68 # }
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69 }
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70 #print "\n\n";
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71 } #end of unless
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72
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73 #Determine models used for each partition, make hash
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74 unless($modelsfile eq 'None'){
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75 open MODFILE, $modelsfile or die "ERROR: Cannot open file $modelsfile\n\n";
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76 while (<MODFILE>) {
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77 chomp;
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78 my $currentinput = "$_";
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79 if($currentinput =~m /\t/){ #must have a tab otherwise wrong file format
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80 if($currentinput =~m /\t\t/){
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81 print OUT "ERROR: file contains 2 tabs in a row. Check phytab format.\n";
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82 die;
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83 }else{
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84 my @genemodel = split(/\t/, $currentinput);
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85 my $genefamily=$genemodel[0];
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86 my $curmodel = $genemodel[1];
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87 if (exists $ModelFor{$genefamily}) {
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88 print OUT "ERROR: Model specification for $genefamily is duplicated\n";
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89 die;
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90 }else{
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91 $ModelFor{$genefamily}=$curmodel;
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92 push(@uniquemodels,$curmodel);
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93 }
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94 }
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95 }else{
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96 die "ERROR: Model LUT must be genefamily\tmodel and contain no blank lines\n";
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97 }
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98 }
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99 }
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100 @uniquemodels = uniq(@uniquemodels); #remove redundant models - uniq is subroutine at end of script
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101
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102 #Now check that models are valid raxml models NOT DONE YET
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103 checkraxmlmodel();
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104
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105 #INPUT ALL DATA
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106 open(INFILE1, $infile1);
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107 foreach $line(<INFILE1>) {
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108 chop($line);
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109 my $getline = $line;
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110 my @column = split(/\t/, $getline);
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111 my $species = $column[0];
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112 my $genefamily = $column[1];
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113 my $genename = $column[2];
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114 my $sequence = $column[3];
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115
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116 if (exists $HoAdatatable{$species}{$genefamily}) {
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117 print OUT "ERROR: $species $genefamily is duplicated\n";
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118 die;
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119 }else{
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120 $HoAdatatable{$species}{$genefamily} = $sequence;
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121 $HoGF{$genefamily}{$species}=$sequence;
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122 }
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123 }
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124
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125 #If no models file selected, set every gene family to GTR model
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126 if($modelsfile eq 'None'){
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127 foreach my $gfkey (sort keys %HoGF){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
128 $ModelFor{$gfkey} = 'GTR';
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
129 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
130 push(@uniquemodels, 'GTR');
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
131 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
132
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
133 #First, keep all species with enough total partitions present
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
134 foreach my $specieskey (sort keys %HoAdatatable)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
135 {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
136 #Count species with minimum gfs
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
137 my $ngf_persp=0;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
138 foreach my $genefamilykey (sort keys %{$HoAdatatable{$specieskey}})
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
139 {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
140 $ngf_persp++;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
141 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
142 unless($ngf_persp < $mingf_persp){ #too few genes for this species, delete the sp
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
143 if($nsl){ #No species list supplied, push all species into list
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
144 push(@specieslist,$specieskey);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
145 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
146 #See if current specieskey is in inputted species list
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
147 my $nsp;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
148 foreach $nsp(@nsp){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
149 if (index($nsp,$specieskey) ge 0){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
150 push(@specieslist,$specieskey);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
151 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
152 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
153 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
154 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
155 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
156 print OUT "\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
157 unless (@specieslist){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
158 print OUT "ERROR: No species with more than $mingf_persp genes\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
159 die;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
160 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
161 if(@specieslist < 4){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
162 print OUT "ERROR: Less than 4 species with more than $mingf_persp genes\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
163 die;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
164 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
165
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
166
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
167 my $oldgenelen = 0;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
168 my $currentseqlen = 0;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
169 foreach my $gfkey (sort keys %HoGF)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
170 {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
171 $oldgenelen=0;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
172 #Count gfs with minimum species
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
173 my $nsp_pergf=0;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
174 for(my $j=0; $j<@specieslist; $j++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
175 if(exists $HoGF{$gfkey}{$specieslist[$j]}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
176 $nsp_pergf++ ; ###if exists $HoGF{$gfkey}{$specieslist[$j]};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
177
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
178
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
179 ##get length of gene and check it is consistent
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
180 if(exists $lengthof{$gfkey}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
181 $currentseqlen = length($HoGF{$gfkey}{$specieslist[$j]});
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
182 # $lengthof{$gfkey} = $currentseqlen;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
183 if($currentseqlen == $oldgenelen){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
184 #$oldgenelen = $lengthof{$gfkey};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
185 #okay
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
186 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
187 print OUT "ERROR: $specieslist[$j] $gfkey sequences ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
188 "different lengths than previous. Sequences must be aligned. If ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
189 "sequences are aligned, check that the line ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
190 "does not have an extra data column before the ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
191 "sequence.\n\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
192 die "ERROR: $specieslist[$j] $gfkey sequences ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
193 "different lengths than previous. Sequences must be aligned. If ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
194 "sequences are aligned, check that the line ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
195 "does not have an extra data column before the ".
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
196 "sequence.\n\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
197 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
198 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
199 $currentseqlen = length($HoGF{$gfkey}{$specieslist[$j]});
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
200 if($currentseqlen == 0){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
201 die "ERROR: Zero length sequence in file.\n"
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
202 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
203 $lengthof{$gfkey} = $currentseqlen;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
204 $oldgenelen = $lengthof{$gfkey};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
205 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
206 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
207 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
208 if($nsp_pergf < $minsp_pergf){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
209 #too few species for this gene family
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
210 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
211 if(exists $lengthof{$gfkey}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
212 if($lengthof{$gfkey}>$min_gf_len){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
213 push(@genelist,$gfkey);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
214 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
215 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
216 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
217 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
218 if (@genelist==0){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
219 print OUT "ERROR: No gene families/partitions meet the specified criteria\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
220 die "ERROR: No gene families/partitions meet the specified criteria\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
221 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
222
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
223 #Now must delete species that lack any *retained* partitions, ie some species may be all missing
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
224 foreach(@specieslist)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
225 {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
226 my $curspecies=$_;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
227 #Count species with minimum gfs
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
228 my $ngf_persp=0;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
229 my $nonmissing=0;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
230 foreach (@genelist)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
231 {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
232 if (exists $HoAdatatable{$curspecies}{$_}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
233 my $cursequence = $HoAdatatable{$curspecies}{$_};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
234 $cursequence =~ s/\?//g;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
235 $cursequence =~ s/\-//g;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
236 #Will not remove N's assumes those are not missing data. Revisit?
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
237 my $curlen = length($cursequence);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
238 $nonmissing = $nonmissing + $curlen;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
239 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
240 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
241 if($nonmissing > 0) #must remove species as it contains none of the genes retained
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
242 {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
243 print "$curspecies has $nonmissing Non-Missing characters\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
244 push(@retainedspecies, $curspecies);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
245 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
246 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
247 @specieslist=@retainedspecies;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
248
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
249 #Remove blankspecies from
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
250 #print phylip file
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
251 #calculate n characters
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
252 my $nchar=0; #total characters
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
253 my $ncharPs =0; #start count for characters in current partition
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
254 my $ncharPe =0; #end count for characters in current partition
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
255
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
256 #First count total characters for first line
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
257 for(my $k=0; $k<@genelist; $k++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
258 if (exists $lengthof{$genelist[$k]}){ #check that length was calculated
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
259 $nchar = $nchar + $lengthof{$genelist[$k]};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
260 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
261 die "ERROR: $genelist[$k] LENGTH MISSING\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
262 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
263 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
264 print OUT @specieslist." ".$nchar."\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
265 htmlheader();
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
266
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
267 #Need to determine gene list order, which will change due to partitioning
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
268 #then write header line of gene names, hopefully in correct order
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
269 #print TABLE "<td bgcolor=white></td>"; #Blank line in species column
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
270 print TABLE "<td style'width:2pc'><font size='-3'>Partition:</td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
271 for(my $part=0; $part < @uniquemodels; $part++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
272 for(my $k=0; $k<@genelist; $k++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
273 #First check if current gf matches current partition
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
274 if(exists $ModelFor{$genelist[$k]}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
275 if($ModelFor{$genelist[$k]} eq $uniquemodels[$part]){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
276 if($ModelFor{$genelist[$k]} eq $uniquemodels[$part]){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
277 print TABLE "<td style'width:2pc'><font size='-3'>$genelist[$k]</td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
278 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
279 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
280 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
281 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
282 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
283 print TABLE "</tr>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
284
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
285 #print TABLE "<td bgcolor=white></td>"; #Blank line in species column
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
286 print TABLE "<td style'width:2pc'><font size='-3'>Model:</td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
287 for(my $part=0; $part < @uniquemodels; $part++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
288 for(my $k=0; $k<@genelist; $k++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
289 #First check if current gf matches current partition
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
290 if(exists $ModelFor{$genelist[$k]}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
291 if($ModelFor{$genelist[$k]} eq $uniquemodels[$part]){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
292 if($ModelFor{$genelist[$k]} eq $uniquemodels[$part]){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
293 print TABLE "<td style'width:2pc'><font size='-3'>$uniquemodels[$part]</td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
294 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
295 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
296 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
297 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
298 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
299 #End of htmlheader printing
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
300
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
301 for(my $j=0; $j<@specieslist; $j++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
302 print OUT "$specieslist[$j]\t";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
303 print TABLE "
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
304 <tr>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
305 <td>$specieslist[$j]</td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
306 for(my $part=0; $part < @uniquemodels; $part++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
307 for(my $k=0; $k<@genelist; $k++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
308 #First check if current gf matches current partition
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
309 if(exists $ModelFor{$genelist[$k]}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
310 if($ModelFor{$genelist[$k]} eq $uniquemodels[$part]){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
311 if (exists $HoAdatatable{$specieslist[$j]}{$genelist[$k]}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
312 print OUT $HoAdatatable{$specieslist[$j]}{$genelist[$k]};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
313 print TABLE "<td bgcolor=black></td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
314 $ncharPe = $ncharPe + $lengthof{$genelist[$k]};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
315 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
316 if (exists $lengthof{$genelist[$k]}){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
317 for(my $gap=0; $gap<$lengthof{$genelist[$k]}; $gap++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
318 print OUT "?";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
319 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
320 $ncharPe = $ncharPe + $lengthof{$genelist[$k]};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
321 print TABLE "<td bgcolor=white></td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
322 #print TABLE "<td style'width:2pc'><font size='-2'>$genelist[$k]</td>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
323 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
324 die "ERROR: BUG!! $genelist[$k] LENGTH MISSING\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
325 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
326 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
327 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
328 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
329 die "ERROR: $genelist[$k] is not assigned a model. Check model LUT input.\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
330 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
331
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
332 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
333 if($j==0){ #print partitions first time through gene lists
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
334 if(($ncharPe==0) || ($ncharPs > $ncharPe)){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
335 push(@nullmodels, $uniquemodels[$part]);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
336 #print "NOTE: no partitions under the model $uniquemodels[$part] made final dataset\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
337 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
338 print PART "$uniquemodels[$part], $uniquemodels[$part] = $ncharPs - $ncharPe \n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
339 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
340 $ncharPs=$ncharPe + 1;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
341 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
342 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
343 print TABLE "</tr>";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
344 print OUT "\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
345 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
346 if($ncharPe/@genelist != $nchar){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
347 # Have to account for multiple times through gene lists -- ncharPe is summed multiple times but printed once
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
348 #die "ERROR: BUG!! Last partition number doesn't match total n characters\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
349 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
350
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
351 #print Statistics to screen can be redirected for Log File
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
352 print "\nSPECIES:\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
353 unless($speciesfile eq 'None'){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
354 print "Used species file to select species. \n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
355 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
356 print "Number of species with $mingf_persp or more genefamilies/partitions: ".@specieslist."\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
357 print "Species list: @specieslist\n\n\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
358 print "\nPARTITIONS/GENE FAMILIES:\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
359 print "Number genefamilies/partitions longer than $min_gf_len characters and present in at least $minsp_pergf genefamilies/partitions: ".@genelist."\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
360 for(my $i=0; $i < @genelist; $i++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
361 print "$genelist[$i] Length:$lengthof{$genelist[$i]}\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
362 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
363
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
364 #Printing Model stats
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
365 print "\nMODELS:\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
366 if($modelsfile eq 'None'){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
367 print "All partitions set to GTR (no model LUT supplied)\n\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
368 }else{
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
369 print "A LUT of models was supplied.\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
370 print "The following models were present in the model LUT file:\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
371 print join(" ", @uniquemodels), "\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
372 print "\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
373 for(my $i=0; $i < @nullmodels; $i++){
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
374 print "NOTE: no partitions under the model $nullmodels[$i] made final dataset\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
375 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
376 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
377 close PART;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
378 close OUT;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
379 close SPFILE;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
380 close TABLE;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
381
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
382 sub uniq {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
383 return keys %{{ map { $_ => 1 } @_ }};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
384 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
385
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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386 sub checkraxmlmodel {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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387 my @raxmlmodels = ("DNA","BIN","MULTI","DAYHOFF", "DCMUT", "JTT", "MTREV", "WAG", "RTREV", "CPREV", "VT", "BLOSUM62", "MTMAM", "LG", "GTR", "MTART", "MTZOA", "FLU","PMB", "HIVB","HIVW","JTTDCMUT");
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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388 return(1); #Not yet implemented
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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389 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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390 sub htmlheader {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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391 print TABLE '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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392 "http://www.w3.org/TR/html4/loose.dtd">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
393 <html>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
394 <head>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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395 <title>Dataset Presences and Absences</title>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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396 <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
397 </head>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
398 <hr><table border="1">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
399 <tr>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
400 <th align="center">Species<br>';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
401 for(my $i=1; $i < @genelist+1; $i++){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
402 #Genes are printing in wrong order
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
403 # print TABLE "<td style'width:2pc'><font size='-2'>$genelist[$i]</td>";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
404 print TABLE "<td style'width:2pc'><font size='-2'>$i</td>";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
405 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
406 print TABLE "</th>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
407 </tr>";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
408 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
409 sub htmltail {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
410 print TABLE '
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
411 </body>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
412 </html>';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
413 }