velvetoptimiser: VelvetOptimiser-2.1.7_modified/VelvetOpt/Utils.pm annotate

annotate VelvetOptimiser-2.1.7_modified/VelvetOpt/Utils.pm @ 0:50ae1360fbbe default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

author	konradpaszkiewicz
date	Tue, 07 Jun 2011 18:07:56 -0400
parents
children

rev	line source
0 50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 # VelvetOpt::Utils.pm
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	3 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4 # Copyright 2008,2009,2010 Simon Gladman <simon.gladman@csiro.au>
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	6 # This program is free software; you can redistribute it and/or modify
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	7 # it under the terms of the GNU General Public License as published by
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	8 # the Free Software Foundation; either version 2 of the License, or
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9 # (at your option) any later version.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	11 # This program is distributed in the hope that it will be useful,
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14 # GNU General Public License for more details.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	16 # You should have received a copy of the GNU General Public License
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	17 # along with this program; if not, write to the Free Software
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	18 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	19 # MA 02110-1301, USA.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	20
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 # Version 2.1.3
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	22
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	23 # Changes for Version 2.0.1
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24 # Added Mikael Brandstrom Durling's numCpus and freeMem for the Mac.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	25 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	26 # Changes for Version 2.1.0
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27 # Fixed bug in estExpCov so it now correctly uses all short read categories not just the first two.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	28 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	29 # Changes for Version 2.1.2
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	30 # Fixed bug in estExpCov so it now won't take columns with "N/A" or "Inf" into account
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	31 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	32 # Changes for Version 2.1.3
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	33 # Changed the minimum contig size to use for estimating expected coverage to 3*kmer size -1 and set the minimum coverage to 2 instead of 0.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	34 # This should get rid of exp_covs of 1 when it should be very high for assembling reads that weren't ampped to a reference using one of the standard read mapping programs
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	35
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	36
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	37 package VelvetOpt::Utils;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	38
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	39 use strict;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	40 use lib "/usr/local/lib/perl5/site_perl/5.8.8";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	41 use warnings;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	42 use POSIX qw(ceil floor);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	43 use Carp;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	44 use List::Util qw(max);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	45 use Bio::SeqIO;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	46
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	47 # num_cpu
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	48 # It returns the number of cpus present in the system if linux.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	49 # If it is MAC then it returns the number of cores present.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	50 # If the OS is not linux or Mac then it returns 1.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	51 # Written by Torsten Seemann 2009 (linux) and Mikael Brandstrom Durling 2009 (Mac).
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	52
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	53 sub num_cpu {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	54 if ( $^O =~ m/linux/i ) {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	55 my ($num) = qx(grep -c ^processor /proc/cpuinfo);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	56 chomp $num;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	57 return $num if $num =~ m/^\d+/;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	58 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	59 elsif( $^O =~ m/darwin/i){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	60 my ($num) = qx(system_profiler SPHardwareDataType \| grep Cores);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	61 $num =~ /.*Cores: (\d+)/;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	62 $num =$1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	63 return $num;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	64 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	65 return 1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	66 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	67
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	68 # free_mem
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	69 # Returns the current amount of free memory
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	70 # Mac Section written by Mikael Brandstrom Durling 2009 (Mac).
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	71
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	72 sub free_mem {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	73 if( $^O =~ m/linux/i ) {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	74 my $x = `free \| grep '^Mem:' \| sed 's/ */~/g' \| cut -d '~' -f 4,7`;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	75 my @tmp = split "~", $x;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	76 my $total = $tmp[0] + $tmp[1];
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	77 my $totalGB = $total / 1024 / 1024;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	78 return $totalGB;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	79 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	80 elsif( $^O =~ m/darwin/i){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	81 my ($tmp) = qx(vm_stat \| grep size);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	82 $tmp =~ /.size of (\d+) bytes./;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	83 my $page_size = $1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	84 ($tmp) = qx(vm_stat \| grep free);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	85 $tmp =~ /[^0-9]+(\d+).*/;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	86 my $free_pages = $1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	87 my $totalGB = ($free_pages * $page_size) / 1024 / 1024 / 1024;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	88 return $totalGB;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	89 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	90 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	91
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	92 # estExpCov
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	93 # it returns the expected coverage of short reads from an assembly by
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	94 # performing a math mode on the stats.txt file supplied.. It looks at
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	95 # all the short_cov? columns.. Uses minimum contig length and minimum coverage.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	96 # needs the stats.txt file path and name, and the k-value used in the assembly.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	97 # Original algorithm by Torsten Seemann 2009 under the GPL.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	98 # Adapted by Simon Gladman 2009.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	99 # It does a weighted mode...
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	100
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	101 sub estExpCov {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	102 use List::Util qw(max);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	103 my $file = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	104 my $kmer = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	105 my $minlen = 3 * $kmer - 1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	106 my $mincov = 2;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	107 my $fh;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	108 unless ( open IN, $file ) {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	109 croak "Unable to open $file for exp_cov determination.\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	110 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	111 my @cov;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	112 while (<IN>) {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	113 chomp;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	114 my @x = split m/\t/;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	115 my $len = scalar @x;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	116 next unless @x >= 7;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	117 next unless $x[1] =~ m/^\d+$/;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	118 next unless $x[1] >= $minlen;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	119
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	120 #add all the short_cov columns..
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	121 my $cov = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	122 for(my $i = 5; $i < $len; $i += 2){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	123 if($x[$i] =~ /\d/){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	124 $cov += $x[$i];
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	125 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	126 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	127 next unless $cov > $mincov;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	128 push @cov, ( ( int($cov) ) x $x[1] );
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	129 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	130
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	131 my %freq_of;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	132 map { $freq_of{$_}++ } @cov;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	133 my $mode = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	134 $freq_of{$mode} = 0; # sentinel
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	135 for my $x ( keys %freq_of ) {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	136 $mode = $x if $freq_of{$x} > $freq_of{$mode};
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	137 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	138 return $mode;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	139 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	140
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	141 # estVelvetMemUse
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	142 # returns the estimated memory usage for velvet in GB
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	143
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	144 sub estVelvetMemUse {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	145 my ($readsize, $genomesize, $numreads, $k) = @_;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	146 my $velvetgmem = -109635 + 18977$readsize + 86326$genomesize + 233353$numreads - 51092$k;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	147 my $out = ($velvetgmem/1024) / 1024;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	148 return $out;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	149 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	150
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	151 # getReadSizeNum
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	152 # returns the number of reads and average size in the short and shortPaired categories...
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	153
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	154 sub getReadSizeNum {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	155 my $f = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	156 my %reads;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	157 my $num = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	158 my $currentfiletype = "fasta";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	159 #first pull apart the velveth string and get the short and shortpaired filenames...
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	160 my @l = split /\s+/, $f;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	161 my $i = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	162 foreach (@l){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	163 if(/^-/){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	164 if(/^-fasta/){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	165 $currentfiletype = "fasta";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	166 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	167 elsif(/^-fastq/){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	168 $currentfiletype = "fastq";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	169 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	170 elsif(/(-eland)\|(-gerald)\|(-fasta.gz)\|(-fastq.gz)/) {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	171 croak "Cannot estimate memory usage from file types other than fasta or fastq..\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	172 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	173 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	174 elsif(-r $_){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	175 my $file = $_;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	176 if($currentfiletype eq "fasta"){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	177 my $x = `grep -c "^>" $file`;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	178 chomp($x);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	179 $num += $x;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	180 my $l = &getReadLength($file, 'Fasta');
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	181 $reads{$l} += $x;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	182 print STDERR "File: $file has $x reads of length $l\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	183 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	184 else {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	185 my $x = `grep -c "^@" $file`;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	186 chomp($x);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	187 $num += $x;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	188 my $l = &getReadLength($file, 'Fastq');
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	189 $reads{$l} += $x;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	190 print STDERR "File: $file has $x reads of length $l\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	191 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	192 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	193 $i ++;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	194 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	195 my $totlength = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	196 foreach my $k (keys %reads){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	197 $totlength += ($reads{$k} * $k);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	198 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	199
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	200
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	201 my @results;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	202 push @results, floor($totlength/$num);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	203 push @results, ($num/1000000);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	204 printf STDERR "Total reads: %.1f million. Avg length: %.1f\n",($num/1000000), ($totlength/$num);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	205 return @results;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	206 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	207
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	208 # getReadLength - returns the length of the first read in a file of type fasta or fastq..
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	209 #
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	210 sub getReadLength {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	211 my ($f, $t) = @_;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	212 my $sio = Bio::SeqIO->new(-file => $f, -format => $t);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	213 my $s = $sio->next_seq() or croak "Something went bad while reading file $f!\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	214 return $s->length;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	215 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	216
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	217 return 1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	218

Mercurial > repos > konradpaszkiewicz > velvetoptimiser

annotate VelvetOptimiser-2.1.7_modified/VelvetOpt/Utils.pm @ 0:50ae1360fbbe default tip