velvetoptimiser: VelvetOptimiser-2.1.7_modified/VelvetOptimiser.pl annotate

annotate VelvetOptimiser-2.1.7_modified/VelvetOptimiser.pl @ 0:7363fee7f20c 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 17:42:26 -0400
parents
children

rev	line source
0 7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 #!/usr/bin/perl -w
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	3 ##Modified by Konrad Paszkiewicz 07/01/2011
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5 # VelvetOptimiser.pl
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	6 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	7 # Copyright 2008, 2009, 2010 Simon Gladman <simon.gladman@csiro.au>
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	8 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9 # This program is free software; you can redistribute it and/or modify
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 # it under the terms of the GNU General Public License as published by
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	11 # the Free Software Foundation; either version 2 of the License, or
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	12 # (at your option) any later version.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	13 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14 # This program is distributed in the hope that it will be useful,
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 # but WITHOUT ANY WARRANTY; without even the implied warranty of
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	17 # GNU General Public License for more details.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	18 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	19 # You should have received a copy of the GNU General Public License
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	20 # along with this program; if not, write to the Free Software
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	22 # MA 02110-1301, USA.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	23
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24 # Version 2.1.7
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	25
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	26 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27 # pragmas
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	28 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	29 use strict;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	30
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	31 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	32 # includes
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	33 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	34 use POSIX qw(strftime);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	35 use FindBin;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	36 use lib "$FindBin::Bin";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	37 use threads;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	38 use threads::shared;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	39 use VelvetOpt::Assembly;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	40 use VelvetOpt::hwrap;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	41 use VelvetOpt::gwrap;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	42 use VelvetOpt::Utils;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	43 use Data::Dumper;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	44 use Storable qw (freeze thaw);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	45 use Getopt::Long;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	46 use lib '/usr/local/lib/perl5/site_perl/5.8.8';
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	47
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	48 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	49 # global var decs
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	50 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	51
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	52 #Change the following integer when compiling Velvet with the MAXKMERLENGTH
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	53 #greater than 31 to the value you used.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	54 my $maxhash;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	55 my @hashvals;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	56 my %assemblies : shared;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	57 my %assembliesObjs;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	58 my @Options;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	59 my $readfile;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	60 my $interested = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	61 my $verbose : shared;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	62 my $hashs;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	63 my $hashe;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	64 my $amos;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	65 my $vgoptions;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	66 my $genomesize;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	67 my @shortInserts;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	68 my $logfile = "logfile.txt";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	69 my $ass_num = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	70 my $categories;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	71 my $prefix;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	72 my $OUT;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	73 my $logSem : shared;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	74 our $num_threads;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	75 my $current_threads : shared = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	76 my $opt_func;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	77 my $opt_func2;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	78 my $OptVersion = "2.1.7";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	79 my $threadfailed : shared = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	80
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	81 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	82 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	83 # main script
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	84 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	85 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	86 print STDERR "
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	87 ****************************************************
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	88
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	89 VelvetOptimiser.pl Version $OptVersion
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	90
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	91 Simon Gladman - CSIRO 2009
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	92
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	93 ****************************************************\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	94
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	95 my $currfreemem = VelvetOpt::Utils::free_mem;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	96
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	97 print STDERR "Number of CPUs available: " . VelvetOpt::Utils::num_cpu . "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	98 printf STDERR "Current free RAM: %.3fGB\n", $currfreemem;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	99
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	100 #get the velveth and velvetg version numbers...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	101 my $response = VelvetOpt::hwrap::_runVelveth(" ");
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	102 $response =~ /Version\s+(\d+\.\d+\.\d+)/s;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	103 my $vhversion = $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	104 unless ($vhversion){ die "Unable to find velveth, please ensure that the velvet executables are in your PATH.\n";}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	105 $response =~ /CATEGORIES = (\d+)/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	106 $categories = $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	107 unless($categories){ $categories = 2; }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	108
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	109 $response =~ /MAXKMERLENGTH = (\d+)/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	110 $maxhash = $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	111 unless($maxhash){ $maxhash = 31; }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	112
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	113 #get the options!
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	114 &setOptions();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	115
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	116 if($prefix eq "auto"){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	117 $logfile = strftime("%d-%m-%Y-%H-%M-%S", localtime) . "_Logfile.txt";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	118 } else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	119 $logfile = $prefix . "_logfile.txt";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	120 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	121
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	122 print "Logfile name: $logfile\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	123
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	124 #open the logfile
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	125 open $OUT, ">$logfile" or die "Couldn't open $logfile for writing.\n$!\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	126
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	127 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	128 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	129 # Perform common tasks - write details to log file and screen, run velveth and vanilla velvetg
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	130 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	131 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	132
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	133 print STDERR "\nMemory use estimation only! Script will terminate after showing results.\n\n" if($genomesize);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	134
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	135 print STDERR "Velvet details:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	136 print STDERR "\tVelvet version: $vhversion\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	137 print STDERR "\tCompiled categories: $categories\n" if $categories;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	138 print STDERR "\tCompiled max kmer length: $maxhash\n" if $maxhash;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	139 print STDERR "\tMaximum number of threads to run: $num_threads\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	140
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	141 #let user know about parameters to run with.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	142 print STDERR "Will run velvet optimiser with the following paramters:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	143 print STDERR "\tVelveth parameter string:\n\t\t$readfile\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	144 print STDERR "\tVelveth start hash values:\t$hashs\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	145 print STDERR "\tVelveth end hash value:\t\t$hashe\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	146 if($vgoptions){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	147 print $OUT "\tUser specified velvetg options: $vgoptions\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	148 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	149 if($amos){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	150 print STDERR "\tRead tracking for final assembly on.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	151 } else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	152 print STDERR "\tRead tracking for final assembly off.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	153 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	154
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	155 #build the hashval array
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	156 for(my $i = $hashs; $i <= $hashe; $i += 2){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	157 push @hashvals, $i;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	158 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	159
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	160 if($genomesize){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	161 my $x = &estMemUse();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	162 printf STDERR "\nMemory use estimated to be: %.1fGB for $num_threads threads.\n\n", $x;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	163 if ($x < $currfreemem){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	164 print STDERR "You should have enough memory to complete this job. (Though this estimate is no guarantee..)\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	165 exit;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	166 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	167 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	168 print STDERR "You probably won't have enough memory to run this job.\nTry decreasing the maximum number of threads used.\n(use the -t option to set max threads.)\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	169 exit;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	170 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	171 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	172
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	173
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	174 print $OUT strftime("%b %e %H:%M:%S", localtime), "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	175
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	176 #send run parameters to log file.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	177 print $OUT "Will run velvet optimiser with the following paramters:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	178 print $OUT "\tVelveth parameter string:\n\t\t$readfile\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	179 print $OUT "\tVelveth start hash values:\t$hashs\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	180 print $OUT "\tVelveth end hash value:\t\t$hashe\n\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	181 if($vgoptions){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	182 print $OUT "\tUser specified velvetg options: $vgoptions\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	183 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	184 if($amos){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	185 print $OUT "\tRead tracking for final assembly on.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	186 } else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	187 print $OUT "\tRead tracking for final assembly off.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	188 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	189
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	190 print STDERR strftime("%b %e %H:%M:%S", localtime), " Beginning velveth runs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	191 print $OUT strftime("%b %e %H:%M:%S", localtime), "\n\n\tBeginning velveth runs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	192
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	193 #now run velveth for all the hashvalues in a certain number of threads..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	194 my @threads;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	195 foreach my $hashval (@hashvals){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	196 while($current_threads >= $num_threads){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	197 sleep(2);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	198 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	199 if($threadfailed){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	200 for my $thr (threads->list) {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	201 #print STDERR "Waiting for thread ",$thr->tid," to complete.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	202 $thr->join;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	203 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	204 die "Velveth failed to run! Must be a problem with file types, check by running velveth manually or by using -v option and reading the log file.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	205 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	206 $threads[$ass_num] = threads->create(\&runVelveth, $readfile, $hashval, $vhversion, \$logSem, $ass_num);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	207 $ass_num ++;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	208 sleep(2);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	209 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	210
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	211 for my $thr (threads->list) {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	212 #print STDERR "Waiting for thread ",$thr->tid," to complete.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	213 $thr->join;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	214 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	215
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	216 #now run velvetg for the all the hashvalues in a certain number of threads..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	217 #first get velvetg's version number.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	218
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	219 $response = VelvetOpt::gwrap::_runVelvetg(" ");
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	220 $response =~ /Version\s+(\d+\.\d+\.\d+)/s;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	221 my $vgversion = $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	222
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	223 print STDERR strftime("%b %e %H:%M:%S", localtime), " Finished velveth runs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	224
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	225 print STDERR strftime("%b %e %H:%M:%S", localtime), " Beginning vanilla velvetg runs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	226 print $OUT strftime("%b %e %H:%M:%S", localtime), "\n\n\tBeginning vanilla velvetg runs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	227
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	228 foreach my $key (sort { $a <=> $b } keys %assemblies){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	229 while($current_threads >= $num_threads){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	230 sleep(2);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	231 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	232 $threads[$ass_num] = threads->create(\&runVelvetg, $vgversion, \$logSem, $key);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	233 sleep(2);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	234 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	235
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	236 for my $thr (threads->list) {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	237 #print STDERR "Waiting for thread ",$thr->tid," to complete.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	238 $thr->join;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	239 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	240
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	241
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	242 #now to thaw it all out..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	243
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	244 foreach my $key(sort keys %assemblies){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	245 my $obj = bless thaw($assemblies{$key}), "VelvetOpt::Assembly";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	246 $assembliesObjs{$key} = $obj;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	247 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	248
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	249
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	250 #find the best assembly...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	251
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	252 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	253 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	254 # Now perform a velvetg optimisation based upon the file types sent to velveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	255 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	256 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	257
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	258 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	259 # get the best assembly so far...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	260 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	261
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	262 my $bestId;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	263 my $maxScore = -100;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	264 my $asmscorenotneg = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	265
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	266 foreach my $key (keys %assembliesObjs){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	267 if(($assembliesObjs{$key}->{assmscore} != -1) && $asmscorenotneg){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	268 if($assembliesObjs{$key}->{assmscore} > $maxScore){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	269 $bestId = $key;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	270 $maxScore = $assembliesObjs{$key}->{assmscore};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	271 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	272 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	273 elsif($assembliesObjs{$key}->{n50} && $asmscorenotneg){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	274 if($assembliesObjs{$key}->{n50} > $maxScore){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	275 $bestId = $key;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	276 $maxScore = $assembliesObjs{$key}->{n50};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	277 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	278 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	279 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	280 $asmscorenotneg = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	281 if($assembliesObjs{$key}->{totalbp} > $maxScore){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	282 $bestId = $key;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	283 $maxScore = $assembliesObjs{$key}->{totalbp};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	284 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	285 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	286 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	287 print "\n\nThe best assembly so far is:\n" if $interested;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	288 print $assembliesObjs{$bestId}->toStringNoV() if $interested;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	289
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	290 # determine the optimisation route for the assembly based on the velveth parameter string.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	291 my $optRoute = &getOptRoutine($readfile);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	292
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	293 print STDERR strftime("%b %e %H:%M:%S", localtime), " Hash value of best assembly by assembly score: ". $assembliesObjs{$bestId}->{hashval} . "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	294
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	295 print $OUT strftime("%b %e %H:%M:%S", localtime), " Best assembly by assembly score - assembly id: $bestId\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	296
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	297 print STDERR strftime("%b %e %H:%M:%S", localtime), " Optimisation routine chosen for best assembly: $optRoute\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	298 print $OUT strftime("%b %e %H:%M:%S", localtime), " Optimisation routine chosen for best assembly: $optRoute\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	299
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	300 #now send the best assembly so far to the appropriate optimisation routine...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	301
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	302 if($optRoute eq "shortOpt"){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	303
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	304 &expCov($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	305 &covCutoff($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	306
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	307 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	308 elsif($optRoute eq "shortLong"){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	309
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	310 &expCov($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	311 &covCutoff($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	312
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	313 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	314 elsif($optRoute eq "longPaired"){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	315 &expCov($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	316 &insLengthLong($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	317 &covCutoff($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	318 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	319 elsif($optRoute eq "shortPaired"){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	320 &expCov($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	321 &insLengthShort($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	322 &covCutoff($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	323 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	324 elsif($optRoute eq "shortLongPaired"){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	325 &expCov($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	326 &insLengthShort($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	327 &insLengthLong($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	328 &covCutoff($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	329 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	330 else{
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	331 print STDERR "There was an error choosing an optimisation routine for this assembly. Please change the velveth parameter string and try again.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	332 print $OUT "There was an error choosing an optimisation routine for this assembly. Please change the velveth parameter string and try again.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	333 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	334
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	335 # once it comes back from the optimisation routines, we need to turn on read tracking and amos output if it was selected in the options.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	336 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	337 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	338 # The final assembly run!
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	339 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	340 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	341 if($amos){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	342 $assembliesObjs{$bestId}->{pstringg} .= " -amos_file yes -read_trkg yes";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	343
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	344 my $final = VelvetOpt::gwrap::objectVelvetg($assembliesObjs{$bestId});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	345 $assembliesObjs{$bestId}->getAssemblyDetails();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	346 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	347
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	348 print STDERR strftime("%b %e %H:%M:%S", localtime), "\n\n\nFinal optimised assembly details:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	349 print $OUT strftime("%b %e %H:%M:%S", localtime), "\n\n\nFinal optimised assembly details:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	350 print STDERR $assembliesObjs{$bestId}->toStringNoV() if !$verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	351 print $OUT $assembliesObjs{$bestId}->toStringNoV() if !$verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	352 print STDERR $assembliesObjs{$bestId}->toString() if $verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	353 print $OUT $assembliesObjs{$bestId}->toString() if $verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	354 print STDERR "\n\nAssembly output files are in the following directory:\n" . $assembliesObjs{$bestId}->{ass_dir} . "\n\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	355 print $OUT "\n\nAssembly output files are in the following directory:\n" . $assembliesObjs{$bestId}->{ass_dir} . "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	356
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	357 #delete superfluous directories..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	358 #Modified by Konrad Paszkiewicz 07/01/2011 - move best results to execution directory for ease of use in Galaxy
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	359 foreach my $key(keys %assemblies){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	360 unless($key == $bestId){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	361 my $dir = $assembliesObjs{$key}->{ass_dir};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	362 `rm -r $dir`;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	363 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	364 if($key==$bestId){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	365 my $dir = $assembliesObjs{$key}->{ass_dir};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	366
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	367 qx(mv $dir/* $dir/../);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	368 `rm -rf $dir`;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	369
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	370 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	371 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	372
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	373
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	374
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	375 # subroutines...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	376 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	377 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	378 #----------------------------------------------------------------------
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	379
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	380 # Option setting routines
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	381
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	382 sub setOptions {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	383 use Getopt::Long;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	384
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	385 my $thmax = VelvetOpt::Utils::num_cpu;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	386
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	387 @Options = (
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	388 {OPT=>"help", VAR=>\&usage, DESC=>"This help"},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	389 {OPT=>"v\|verbose+", VAR=>\$verbose, DEFAULT=>0, DESC=>"Verbose logging, includes all velvet output in the logfile."},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	390 {OPT=>"s\|hashs=i", VAR=>\$hashs, DEFAULT=>19, DESC=>"The starting (lower) hash value"},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	391 {OPT=>"e\|hashe=i", VAR=>\$hashe, DEFAULT=>31, DESC=>"The end (higher) hash value"},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	392 {OPT=>"f\|velvethfiles=s", VAR=>\$readfile, DEFAULT=>0, DESC=>"The file section of the velveth command line."},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	393 {OPT=>"a\|amosfile!", VAR=>\$amos, DEFAULT=>0, DESC=>"Turn on velvet's read tracking and amos file output."},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	394 {OPT=>"o\|velvetgoptions=s", VAR=>\$vgoptions, DEFAULT=>'', DESC=>"Extra velvetg options to pass through. eg. -long_mult_cutoff -max_coverage etc"},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	395 {OPT=>"t\|threads=i", VAR=>\$num_threads, DEFAULT=>$thmax, DESC=>"The maximum number of simulataneous velvet instances to run."},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	396 {OPT=>"g\|genomesize=f", VAR=>\$genomesize, DEFAULT=>0, DESC=>"The approximate size of the genome to be assembled in megabases.\n\t\t\tOnly used in memory use estimation. If not specified, memory use estimation\n\t\t\twill not occur. If memory use is estimated, the results are shown and then program exits."},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	397 {OPT=>"k\|optFuncKmer=s", VAR=>\$opt_func, DEFAULT=>'n50', DESC=>"The optimisation function used for k-mer choice."},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	398 {OPT=>"c\|optFuncCov=s", VAR=>\$opt_func2, DEFAULT=>'Lbp', DESC=>"The optimisation function used for cov_cutoff optimisation."},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	399 {OPT=>"p\|prefix=s", VAR=>\$prefix, DEFAULT=>'auto', DESC=>"The prefix for the output filenames, the default is the date and time in the format DD-MM-YYYY-HH-MM_."}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	400 );
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	401
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	402 (@ARGV < 1) && (usage());
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	403
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	404 &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) \|\| usage();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	405
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	406 # Now setup default values.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	407 foreach (@Options) {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	408 if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	409 ${$_->{VAR}} = $_->{DEFAULT};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	410 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	411 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	412
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	413 print STDERR strftime("%b %e %H:%M:%S", localtime), " Starting to check input parameters.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	414
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	415 unless($readfile){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	416 print STDERR "\tYou must supply the velveth parameter line in quotes. eg -f '-short .....'\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	417 &usage();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	418 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	419
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	420 if($hashs > $maxhash){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	421 print STDERR "\tStart hash value too high. New start hash value is $maxhash.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	422 $hashs = $maxhash;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	423 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	424 if(!&isOdd($hashs)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	425 $hashs = $hashs - 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	426 print STDERR "\tStart hash value not odd. Subtracting one. New start hash value = $hashs\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	427 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	428
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	429 if($hashe > $maxhash \|\| $hashe < 1){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	430 print STDERR "\tEnd hash value not in workable range. New end hash value is $maxhash.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	431 $hashe = $maxhash;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	432 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	433 if($hashe < $hashs){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	434 print STDERR "\tEnd hash value lower than start hash value. New end hash value = $hashs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	435 $hashe = $hashs;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	436 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	437 if(!&isOdd($hashe)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	438 $hashe = $hashe - 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	439 print STDERR "\tEnd hash value not odd. Subtracting one. New end hash value = $hashe\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	440 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	441
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	442 #check the velveth parameter string..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	443 my $vh_ok = VelvetOpt::hwrap::_checkVHString("check 21 $readfile", $categories);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	444
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	445 unless($vh_ok){ die "Please re-start with a corrected velveth parameter string." }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	446
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	447 print STDERR "\tVelveth parameter string OK.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	448
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	449 print STDERR strftime("%b %e %H:%M:%S", localtime), " Finished checking input parameters.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	450
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	451 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	452
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	453 sub usage {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	454 print "Usage: $0 [options] -f 'velveth input line'\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	455 foreach (@Options) {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	456 printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	457 defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	458 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	459 print "\nAdvanced!: Changing the optimisation function(s)\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	460 print VelvetOpt::Assembly::opt_func_toString;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	461 exit(1);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	462 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	463
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	464 #----------------------------------------------------------------------
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	465
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	466
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	467 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	468 # runVelveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	469 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	470
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	471 sub runVelveth{
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	472
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	473 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	474 lock($current_threads);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	475 $current_threads ++;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	476 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	477
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	478 my $rf = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	479 my $hv = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	480 my $vv = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	481 my $semRef = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	482 my $anum = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	483 my $assembly;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	484
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	485 print STDERR strftime("%b %e %H:%M:%S", localtime), "\t\tRunning velveth with hash value: $hv.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	486
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	487 #make the velveth command line.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	488 my $vhline = $prefix . "_data_$hv $hv $rf";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	489
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	490 #make a new VelvetAssembly and store it in the %assemblies hash...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	491 $assembly = VelvetOpt::Assembly->new(ass_id => $anum, pstringh => $vhline, versionh =>$vv, assmfunc => $opt_func, assmfunc2 => $opt_func2);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	492
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	493 #run velveth on this assembly object
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	494 my $vhresponse = VelvetOpt::hwrap::objectVelveth($assembly, $categories);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	495
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	496 unless($vhresponse){ die "Velveth didn't run on hash value of $hv.\n$!\n";}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	497
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	498 unless(-r ($prefix . "_data_$hv" . "/Roadmaps")){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	499 print STDERR "Velveth failed! Response:\n$vhresponse\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	500 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	501 lock ($threadfailed);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	502 $threadfailed = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	503 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	504 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	505
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	506 #run the hashdetail generation routine.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	507 $vhresponse = $assembly->getHashingDetails();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	508
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	509 #print the objects to the log file...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	510 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	511 lock($$semRef);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	512 print $OUT $assembly->toStringNoV() if !$verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	513 print $OUT $assembly->toString() if $verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	514 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	515
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	516 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	517 lock(%assemblies);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	518 my $ass_str = freeze($assembly);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	519 $assemblies{$anum} = $ass_str;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	520 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	521
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	522 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	523 lock($current_threads);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	524 $current_threads --;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	525 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	526 print STDERR strftime("%b %e %H:%M:%S", localtime), "\t\tVelveth with hash value $hv finished.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	527 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	528
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	529 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	530 # runVelvetg
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	531 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	532 sub runVelvetg{
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	533
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	534 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	535 lock($current_threads);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	536 $current_threads ++;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	537 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	538
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	539 my $vv = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	540 my $semRef = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	541 my $anum = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	542 my $assembly;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	543
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	544 #get back the object!
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	545 $assembly = bless thaw($assemblies{$anum}), "VelvetOpt::Assembly";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	546
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	547 print STDERR strftime("%b %e %H:%M:%S", localtime), "\t\tRunning vanilla velvetg on hash value: " . $assembly->{hashval} . "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	548
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	549 #make the velvetg commandline.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	550 my $vgline = $prefix . "_data_" . $assembly->{hashval};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	551
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	552 $vgline .= " $vgoptions";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	553
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	554 #save the velvetg commandline in the assembly.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	555 $assembly->{pstringg} = $vgline;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	556
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	557 #save the velvetg version in the assembly.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	558 $assembly->{versiong} = $vv;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	559
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	560 #run velvetg
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	561 my $vgresponse = VelvetOpt::gwrap::objectVelvetg($assembly);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	562
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	563 unless($vgresponse){ die "Velvetg didn't run on the directory $vgline.\n$!\n";}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	564
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	565 #run the assembly details routine..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	566 $assembly->getAssemblyDetails();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	567
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	568 #print the objects to the log file...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	569 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	570 lock($$semRef);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	571 print $OUT $assembly->toStringNoV() if !$verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	572 print $OUT $assembly->toString() if $verbose;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	573 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	574
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	575 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	576 lock(%assemblies);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	577 my $ass_str = freeze($assembly);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	578 $assemblies{$anum} = $ass_str;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	579 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	580
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	581 {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	582 lock($current_threads);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	583 $current_threads --;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	584 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	585 print STDERR strftime("%b %e %H:%M:%S", localtime), "\t\tVelvetg on hash value: " . $assembly->{hashval} . " finished.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	586 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	587
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	588 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	589 # isOdd
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	590 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	591 sub isOdd {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	592 my $x = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	593 if($x % 2 == 1){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	594 return 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	595 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	596 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	597 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	598 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	599 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	600
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	601
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	602 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	603 # getOptRoutine
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	604 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	605 sub getOptRoutine {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	606
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	607 my $readfile = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	608
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	609 # Choose the optimisation path depending on the types of read files sent to velveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	610 # For short only: shortOpt routine
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	611 # For short and long: shortLong routine
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	612 # For short paired: shortPaired routine
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	613 # For short and long paired: longPaired routine
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	614 # For short paired and long: shortPaired routine
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	615 # For short paired & long paired: shortlongPaired routine
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	616
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	617 #look at velveth string ($readfile) and look for keywords from velvet manual...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	618 my $long = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	619 my $longPaired = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	620 my $shortPaired = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	621 my $short = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	622
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	623 #standard cases..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	624 if($readfile =~ /-short.? /) { $short = 1; }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	625 if($readfile =~ /-long /) { $long = 1; }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	626 if($readfile =~ /-shortPaired /) { $shortPaired = 1; }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	627 if($readfile =~ /-longPaired /) { $longPaired = 1; }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	628
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	629 #weird cases to cover the non-use of the short keyword (since its the default.)
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	630 if(!($readfile =~ /(-short.? )\|(-long )\|(-shortPaired )\|(-longPaired )/)) { $short = 1; } #if nothing is specified, assume short.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	631 if(!($readfile =~ /-short.? /) && ($readfile =~ /(-long )\|(-longPaired )/)) { $short = 1; } #if long or longPaired is specified, also assum short since very unlikely to only have long...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	632
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	633 if($short && !($long \|\| $longPaired \|\| $shortPaired)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	634 return "shortOpt";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	635 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	636 elsif($short && $long && !($longPaired \|\| $shortPaired)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	637 return "shortLong";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	638 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	639 elsif($short && $longPaired && !$shortPaired){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	640 return "longPaired";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	641 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	642 elsif($short && $shortPaired && !$longPaired){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	643 return "shortPaired";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	644 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	645 elsif($short && $shortPaired && $longPaired){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	646 return "shortLongPaired";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	647 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	648 elsif($shortPaired && !$short && !$long && !$longPaired){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	649 return "shortPaired";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	650 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	651 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	652 return "Unknown";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	653 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	654 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	655
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	656 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	657 # covCutoff - the coverage cutoff optimisation routine.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	658 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	659 sub covCutoff{
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	660
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	661 my $ass = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	662 #get the assembly score and set the current cutoff score.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	663 my $ass_score = $ass->{assmscore};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	664 print "In covCutOff and assembly score is: $ass_score..\n" if $interested;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	665
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	666
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	667
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	668 sub func {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	669 my $ass = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	670 my $cutoff = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	671 my $ass_score = $ass->{assmscore};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	672 my $ps = $ass->{pstringg};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	673 if($ps =~ /cov_cutoff/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	674 $ps =~ s/cov_cutoff\s+\d+(\.\d+)?/cov_cutoff $cutoff/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	675 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	676 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	677 $ps .= " -cov_cutoff $cutoff";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	678 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	679 $ass->{pstringg} = $ps;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	680
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	681 print STDERR strftime("%b %e %H:%M:%S", localtime);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	682 printf STDERR "\t\tSetting cov_cutoff to %.3f.\n", $cutoff;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	683 print $OUT strftime("%b %e %H:%M:%S", localtime);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	684 printf $OUT "\t\tSetting cov_cutoff to %.3f.\n", $cutoff;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	685
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	686 my $worked = VelvetOpt::gwrap::objectVelvetg($ass);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	687 if($worked){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	688 $ass->getAssemblyDetails();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	689 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	690 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	691 die "Velvet Error in covCutoff!\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	692 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	693 $ass_score = $ass->{assmscore};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	694 print $OUT $ass->toStringNoV();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	695
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	696 return $ass_score;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	697
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	698 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	699
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	700 print STDERR strftime("%b %e %H:%M:%S", localtime), " Beginning coverage cutoff optimisation\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	701 print $OUT strftime("%b %e %H:%M:%S", localtime), " Beginning coverage cutoff optimisation\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	702
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	703 my $dir = $ass->{ass_dir};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	704 $dir .= "/stats.txt";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	705 #print "\tLooking for exp_cov in $dir\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	706 my $expCov = VelvetOpt::Utils::estExpCov($dir, $ass->{hashval});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	707
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	708 my $a = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	709 my $b = 0.8 * $expCov;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	710 my $t = 0.618;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	711 my $c = $a + $t * ($b - $a);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	712 my $d = $b + $t * ($a - $b);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	713 my $fc = func($ass, $c);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	714 my $fd = func($ass, $d);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	715
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	716 my $iters = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	717
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	718 printf STDERR "\t\tLooking for best cutoff score between %.3f and %.3f\n", $a, $b;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	719 printf $OUT "\t\tLooking for best cutoff score between %.3f and %.3f\n", $a, $b;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	720
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	721 while(abs($a -$b) > 1){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	722 if($fc > $fd){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	723 printf STDERR "\t\tMax cutoff lies between %.3f & %.3f\n", $d, $b;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	724 my $absdiff = abs($fc - $fd);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	725 print STDERR "\t\tfc = $fc\tfd = $fd\tabs diff = $absdiff\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	726 printf $OUT "\t\tMax cutoff lies between %.3f & %.3f\n", $d, $b;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	727 $a = $d;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	728 $d = $c;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	729 $fd = $fc;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	730 $c = $a + $t * ($b - $a);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	731 $fc = func($ass, $c);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	732 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	733 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	734 printf STDERR "\t\tMax cutoff lies between %.3f & %.3f\n", $a, $c;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	735 my $absdiff = abs($fc - $fd);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	736 print STDERR "\t\tfc = $fc\tfd = $fd\tabs diff = $absdiff\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	737 printf $OUT "\t\tMax cutoff lies between %.3f & %.3f\n", $a, $c;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	738 $b = $c;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	739 $c = $d;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	740 $fc = $fd;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	741 $d = $b + $t * ($a - $b);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	742 $fd = func($ass, $d);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	743 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	744 $iters ++;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	745 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	746
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	747 printf STDERR "\t\tOptimum value of cutoff is %.2f\n", $b;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	748 print STDERR "\t\tTook $iters iterations\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	749 printf $OUT "\t\tOptimum value of cutoff is %.2f\n", $b;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	750 print $OUT "\t\tTook $iters iterations\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	751
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	752 return 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	753
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	754 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	755
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	756 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	757 # expCov - find the expected coverage for the assembly and run velvetg with that exp_cov.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	758 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	759 sub expCov {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	760
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	761 print STDERR strftime("%b %e %H:%M:%S", localtime), " Looking for the expected coverage\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	762 print $OUT strftime("%b %e %H:%M:%S", localtime), " Looking for the expected coverage\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	763
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	764 my $ass = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	765
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	766 #need to get the directory of the assembly and add "stats.txt" to it and then send it to
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	767 #the histogram methods in SlugsUtils.pm...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	768 my $dir = $ass->{ass_dir};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	769 $dir .= "/stats.txt";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	770 my $expCov = VelvetOpt::Utils::estExpCov($dir, $ass->{hashval});
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	771
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	772 print STDERR strftime("%b %e %H:%M:%S", localtime), "\t\tExpected coverage set to $expCov\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	773 print $OUT strftime("%b %e %H:%M:%S", localtime), "\t\tExpected coverage set to $expCov\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	774
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	775 #re-write the pstringg with the new velvetg command..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	776 my $vg = $ass->{pstringg};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	777 if($vg =~ /exp_cov/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	778 $vg =~ s/exp_cov\s+\d+/exp_cov $expCov/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	779 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	780 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	781 $vg .= " -exp_cov $expCov";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	782 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	783
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	784 $ass->{pstringg} = $vg;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	785
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	786 print $OUT $ass->toStringNoV();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	787
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	788 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	789
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	790 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	791 # insLengthLong - get the Long insert length and use it in the assembly..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	792 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	793 sub insLengthLong {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	794 print STDERR strftime("%b %e %H:%M:%S", localtime), " Getting the long insert length\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	795 print $OUT strftime("%b %e %H:%M:%S", localtime), " Getting the long insert length\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	796 my $ass = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	797 my $len = "auto";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	798 print STDERR strftime("%b %e %H:%M:%S", localtime), " Setting assembly long insert length $len\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	799 print $OUT strftime("%b %e %H:%M:%S", localtime), " Setting assembly long insert length $len\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	800
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	801 #re-write the pstringg with the new velvetg command..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	802 #my $vg = $ass->{pstringg};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	803 #if($vg =~ /ins_length_long/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	804 # $vg =~ s/ins_length_long\s+\d+/ins_length_long $len/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	805 #}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	806 #else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	807 # $vg .= " -ins_length_long $len";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	808 #}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	809 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	810
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	811 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	812 # insLengthShort - get the short insert length and use it in the assembly..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	813 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	814 sub insLengthShort {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	815 print STDERR strftime("%b %e %H:%M:%S", localtime), " Setting the short insert length\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	816 print $OUT strftime("%b %e %H:%M:%S", localtime), " Setting the short insert length\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	817 my $ass = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	818 my $len = "auto";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	819 print STDERR strftime("%b %e %H:%M:%S", localtime), " Setting assembly short insert length(s) to $len\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	820 print $OUT strftime("%b %e %H:%M:%S", localtime), " Setting assembly short insert length(s) to $len\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	821
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	822 #re-write the pstringg with the new velvetg command..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	823 #my $vg = $ass->{pstringg};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	824 #if($vg =~ /ins_length /){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	825 # $vg =~ s/ins_length\s+\d+/ins_length $len/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	826 #}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	827 #else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	828 # $vg .= " -ins_length $len";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	829 #}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	830 #$ass->{pstringg} = $vg;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	831 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	832
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	833
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	834 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	835 # estMemUse - estimates the memory usage from
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	836 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	837 sub estMemUse {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	838
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	839 my $max_runs = @hashvals;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	840 my $totmem = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	841 #get the read lengths and the number of reads...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	842 #need the short read filenames...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	843 my ($rs, $nr) = VelvetOpt::Utils::getReadSizeNum($readfile);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	844 if ($max_runs > $num_threads){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	845 for(my $i = 0; $i < $num_threads; $i ++){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	846 $totmem += VelvetOpt::Utils::estVelvetMemUse($rs, $genomesize, $nr, $hashvals[$i]);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	847 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	848 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	849 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	850 foreach my $h (@hashvals){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	851 $totmem += VelvetOpt::Utils::estVelvetMemUse($rs, $genomesize, $nr, $h);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	852 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	853 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	854 return $totmem;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	855 }

Mercurial > repos > konradpaszkiewicz > velvetoptimiser

annotate VelvetOptimiser-2.1.7_modified/VelvetOptimiser.pl @ 0:7363fee7f20c default tip