Mercurial > repos > dereeper > sniplay
view egglib/CalculateDiversityIndexes.pl @ 4:10627af23f10 draft
planemo upload
author | gandres |
---|---|
date | Tue, 15 Dec 2015 05:18:02 -0500 |
parents | 420b57c3c185 |
children |
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#!/usr/bin/perl use strict; use Switch; use Getopt::Long; use Bio::SeqIO; my $usage = qq~Usage:$0 <args> [<opts>] where <args> are: -i, --input <FASTA input> -o, --output <output filename> -d, --directory <directory of egglib package> ~; $usage .= "\n"; my ($infile,$outfile,$dir_exe); GetOptions( "input=s" => \$infile, "output=s" => \$outfile, "directory=s"=> \$dir_exe ); die $usage if ( !$infile || !$outfile || !$dir_exe); my $EGGSTATS_EXE = "$dir_exe/egglib-2.1.5/bin/eggstats"; my %gene_alignments; my $in = Bio::SeqIO->new(-file => $infile , '-format' => 'Fasta'); while ( my $seq = $in->next_seq() ) { my $id = $seq -> id(); my $sequence = $seq -> seq(); my ($gene,$ind,$num_allele) = split("_",$id); $gene_alignments{$gene}.= ">$id\n$sequence\n"; } open(OUT,">$outfile"); foreach my $gene(keys(%gene_alignments)) { open(F,">$gene.egglib_input.fa"); print F $gene_alignments{$gene}; close(F); my $results_egglib = `$EGGSTATS_EXE $gene.egglib_input.fa`; # parse Seqlib output if ($results_egglib) { my %egglig_stats; my @eggstats = split(/^/,$results_egglib); foreach my $eggstat(@eggstats) { my ($desc,$value) = split(/: /,$eggstat); chomp($value); $egglig_stats{$desc} = $value; } print OUT "$gene;"; print OUT $egglig_stats{"Total number of sequences"} . ";"; print OUT $egglig_stats{"Total number of sites"} . ";"; print OUT $egglig_stats{"Number of analyzed sites"} . ";"; print OUT $egglig_stats{"S"} . ";"; print OUT $egglig_stats{"thetaW"} . ";"; print OUT $egglig_stats{"Pi"} . ";"; print OUT $egglig_stats{"D"} . ";"; print OUT $egglig_stats{"number of haplotypes"} . ";"; print OUT $egglig_stats{"haplotypes diversity"} . ";"; print OUT $egglig_stats{"Fay and Wu H"} . ";"; print OUT $egglig_stats{"Fst"} . ";"; print OUT $egglig_stats{"Snn"} . ";"; print OUT "\n"; unlink("$gene.egglib_input.fa"); } } close(OUT);