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

annotate VelvetOptimiser-2.1.7_modified/VelvetOpt/Assembly.pm @ 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 # VelvetOpt::Assembly.pm
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 # Copyright 2008,2009 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	4 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5 # 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	6 # 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	7 # 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	8 # (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	9 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 # 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	11 # 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	12 # 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	13 # 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	14 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 # 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	16 # 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	17 # 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	18 # 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	19
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	20 # Version 2.1.2
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	22 # Changes for 2.0.1
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	23 # *Bug fix in CalcAssemblyScore. Now returns 0 if there is no calculable score instead of crashing.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	25 # Changes for 2.1.0
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	26 # *Added 2 stage optimisation functions for optimising kmer size and cov_cutoff differently if required.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	28 # Changes for 2.1.1
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	29 # *Allowed for non-word characters in prefix names. (. - etc.) Still no spaces allowed in prefix name or any filenames.
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 # Changes for 2.1.2
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	32 # *Now warns nicely of optimisation function returning undef or 0. Suggests you choose and alternative.
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 # Changes for 2.1.3
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	35 # *Now prints the velvet calculated insert sizes and standard deviations in the Assembly summaries (both log files and screen).
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	36
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	37 package VelvetOpt::Assembly;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	38
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	39 =head1 NAME
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	40
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	41 VelvetOpt::Assembly.pm - Velvet assembly container class.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	42
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	43 =head1 AUTHOR
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	44
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	45 Simon Gladman, CSIRO, 2007, 2008.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	46
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	47 =head1 LICENSE
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 Copyright 2008, 2009 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	50
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	51 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	52 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	53 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	54 (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	55
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	56 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	57 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	58 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	59 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	60
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	61 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	62 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	63 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	64 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	65
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	66 =head1 SYNOPSIS
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	67
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	68 use VelvetOpt::Assembly;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	69 my $object = VelvetOpt::Assembly->new(
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	70 timestamph => "23 November 2008 15:00:00",
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	71 ass_id => "1",
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	72 versionh => "0.7.04",
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	73 ass_dir => "/home/gla048/Desktop/newVelvetOptimiser/data_1"
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	74 );
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	75 print $object->toString();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	76
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	77 =head1 DESCRIPTION
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	78
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	79 A container class to hold the results of a Velvet assembly. Includes timestamps,
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	80 version information, parameter strings and assembly output metrics.
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 Version 1.1
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	83
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	84 =head2 Uses
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 =over 8
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 =item strict
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	89
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	90 =item warnings
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	91
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	92 =item Carp
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	93
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	94 =back
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	95
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	96 =head2 Fields
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	97
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	98 =over 8
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 =item assmscore
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	101
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	102 The assembly score metric for this object
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	103
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	104 =item timstamph
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	105
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	106 The timestamp of the start of the velveth run for this assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	107
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	108 =item timestampg
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	109
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	110 The date and time of the end of the velvetg run.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	111
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	112 =item ass_id
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	113
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	114 The assembly id number. Sequential for all the runs for this optimisation.
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 =item versionh
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	117
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	118 The version number of velveth used in this assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	119
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	120 =item versiong
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 The version number of velvetg used in this assembly
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 =item readfilename
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	125
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	126 The name of the file containing all the reads (or a qw of them if more than one...)
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 =item pstringh
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	129
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	130 The velveth parameter string used in this assembly
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 =item pstringg
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	133
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	134 The velvetg parameter string used in this assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	135
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	136 =item ass_dir
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	137
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	138 The assembly directory path (full)
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	139
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	140 =item hashval
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	141
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	142 The hash value used for this assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	143
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	144 =item rmapfs
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	145
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	146 The roadmap file size
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	147
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	148 =item sequences
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	149
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	150 The total number of sequences in the input files
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	151
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	152 =item nconts
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 The number of contigs in the final assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	155
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	156 =item totalbp
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	157
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	158 The total number of bases in the contigs
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 =item n50
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	161
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	162 The n50 of the assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	163
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	164 =item maxlength
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	165
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	166 The length of the longest contig in the assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	167
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	168 =item maxcont
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	169
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	170 The size of the largest contig in the assembly
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 =item nconts1k
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 The number of contigs greater than 1k in size
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 =item totalbp1k
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	177
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	178 the sum of the length of contigs > 1k in size
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	179
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	180 =item velvethout
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	181
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	182 The velveth output
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 =item velvetgout
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	185
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	186 The velvetg output
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	187
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	188 =back
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 =head2 Methods
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	191
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	192 =over 8
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	193
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	194 =item new
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	195
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	196 Returns a new VelvetAssembly object.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	197
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	198 =item accessor methods
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	199
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	200 Accessor methods for all fields.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	201
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	202 =item calcAssemblyScore
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 Calculates the assembly score of the object (after velvetg has been run.) and stores it in self.
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 =item getHashingDetails
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	207
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	208 Gets the details of the outputs from the velveth run and stores it in self.
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 =item getAssemblyDetails
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	211
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	212 Gets the details of the outputs from the velvetg run and stores it in self.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	213
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	214 =item toString
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 Returns a string representation of the object's contents.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	217
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	218 =item toStringNoV
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	219
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	220 Returns a string representation of the object's contents without the velvet outputs which are large.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	221
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	222 =item opt_func_toString
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	223
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	224 Returns the usage of the optimisation function.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	225
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	226 =back
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 =cut
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	229
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	230 use strict;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	231 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	232 use Carp;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	233 use warnings;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	234 #use base "Storable";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	235 use Cwd;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	236 use Bio::SeqIO;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	237
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	238 my $interested = 0;
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 #constructor
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	243 sub new {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	244 my $class = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	245 my $self = {@_};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	246 bless ($self, $class);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	247 return $self;
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 #optimisation function options...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	251 my %f_opts;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	252 $f_opts{'ncon'}->{'intname'} = 'nconts';
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	253 $f_opts{'ncon'}->{'desc'} = "The total number of contigs";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	254 $f_opts{'n50'}->{'intname'} = 'n50';
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	255 $f_opts{'n50'}->{'desc'} = "The n50";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	256 $f_opts{'max'}->{'intname'} = 'maxlength';
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	257 $f_opts{'max'}->{'desc'} = "The length of the longest contig";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	258 $f_opts{'Lcon'}->{'intname'} = 'nconts1k';
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	259 $f_opts{'Lcon'}->{'desc'} = "The number of large contigs";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	260 $f_opts{'tbp'}->{'intname'} = 'totalbp';
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	261 $f_opts{'tbp'}->{'desc'} = "The total number of basepairs in contigs";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	262 $f_opts{'Lbp'}->{'intname'} = 'totalbp1k';
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	263 $f_opts{'Lbp'}->{'desc'} = "The total number of base pairs in large contigs";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	264
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	265 #accessor methods
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	266 sub assmscore{ $_[0]->{assmscore}=$_[1] if defined $_[1]; $_[0]->{assmscore}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	267 sub timestamph{ $_[0]->{timestamph}=$_[1] if defined $_[1]; $_[0]->{timestamph}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	268 sub timestampg{ $_[0]->{timestampg}=$_[1] if defined $_[1]; $_[0]->{timestampg}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	269 sub ass_id{ $_[0]->{ass_id}=$_[1] if defined $_[1]; $_[0]->{ass_id}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	270 sub versionh{ $_[0]->{versionh}=$_[1] if defined $_[1]; $_[0]->{versionh}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	271 sub versiong{ $_[0]->{versiong}=$_[1] if defined $_[1]; $_[0]->{versiong}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	272 sub readfilename{ $_[0]->{readfilename}=$_[1] if defined $_[1]; $_[0]->{readfilename}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	273 sub pstringh{ $_[0]->{pstringh}=$_[1] if defined $_[1]; $_[0]->{pstringh}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	274 sub pstringg{ $_[0]->{pstringg}=$_[1] if defined $_[1]; $_[0]->{pstringg}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	275 sub ass_dir{ $_[0]->{ass_dir}=$_[1] if defined $_[1]; $_[0]->{ass_dir}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	276 sub hashval{ $_[0]->{hashval}=$_[1] if defined $_[1]; $_[0]->{hashval}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	277 sub rmapfs{ $_[0]->{rmapfs}=$_[1] if defined $_[1]; $_[0]->{rmapfs}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	278 sub nconts{ $_[0]->{nconts}=$_[1] if defined $_[1]; $_[0]->{nconts}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	279 sub n50{ $_[0]->{n50}=$_[1] if defined $_[1]; $_[0]->{n50}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	280 sub maxlength{ $_[0]->{maxlength}=$_[1] if defined $_[1]; $_[0]->{maxlength}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	281 sub nconts1k{ $_[0]->{nconts1k}=$_[1] if defined $_[1]; $_[0]->{nconts1k}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	282 sub totalbp{ $_[0]->{totalbp}=$_[1] if defined $_[1]; $_[0]->{totalbp}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	283 sub totalbp1k{ $_[0]->{totalbp1k}=$_[1] if defined $_[1]; $_[0]->{totalbp1k}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	284 sub velvethout{ $_[0]->{velvethout}=$_[1] if defined $_[1]; $_[0]->{velvethout}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	285 sub velvetgout{ $_[0]->{velvetgout}=$_[1] if defined $_[1]; $_[0]->{velvetgout}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	286 sub sequences{ $_[0]->{sequences}=$_[1] if defined $_[1]; $_[0]->{sequences}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	287 sub assmfunc{ $_[0]->{assmfunc}=$_[1] if defined $_[1]; $_[0]->{assmfunc}}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	288 sub assmfunc2{ $_[0]->{assmfunc2}=$_[1] if defined $_[1]; $_[0]->{assmfunc2}}
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 #assemblyScoreCalculator
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	291 sub calcAssemblyScore {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	292 use Safe;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	293
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	294 my $self = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	295 my $func = shift;
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 my $cpt = new Safe;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	298
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	299 #Basic variable IO and traversal
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	300 $cpt->permit(qw(null scalar const padany lineseq leaveeval rv2sv rv2hv helem hslice each values keys exists delete rv2cv));
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	301 #Comparators
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	302 $cpt->permit(qw(lt i_lt gt i_gt le i_le ge i_ge eq i_eq ne i_ne ncmp i_ncmp slt sgt sle sge seq sne scmp));
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	303 #Base math
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	304 $cpt->permit(qw(preinc i_preinc predec i_predec postinc i_postinc postdec i_postdec int hex oct abs pow multiply i_multiply divide i_divide modulo i_modulo add i_add subtract i_subtract));
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	305 #Binary math
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	306 $cpt->permit(qw(left_shift right_shift bit_and bit_xor bit_or negate i_negate not complement));
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	307 #Regex
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	308 $cpt->permit(qw(match split qr));
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	309 #Conditionals
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	310 $cpt->permit(qw(cond_expr flip flop andassign orassign and or xor));
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	311 #Advanced math
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	312 $cpt->permit(qw(atan2 sin cos exp log sqrt rand srand));
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 foreach my $key (keys %f_opts){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	315 print "\nkey: $key\tintname: ", $f_opts{$key}->{'intname'}, "\n" if $interested;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	316
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	317 $func =~ s/\b$key\b/$self->{$f_opts{$key}->{'intname'}}/g;
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
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	320 my $r = $cpt->reval($func);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	321 warn $@ if $@;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	322 $self->{assmscore} = $r;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	323 unless($r =~ /^\d+/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	324 warn "Optimisation function did not return a single float.\nOptimisation function was not evaluatable.\nOptfunc: $func";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	325 warn "Setting assembly score to 0\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	326 $self->{assmscore} = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	327 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	328 if($r == 0){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	329 print STDERR "**********\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	330 print STDERR "Warning: Assembly score for assembly_id " . $self->{ass_id} . " is 0\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	331 print STDERR "You may want to consider choosing a different optimisation variable or function.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	332 print STDERR "Current optimisation functions are ", $self->{assmfunc}, " for k value and ", $self->{assmfunc2}, " for cov_cutoff\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	333 print STDERR "**********\n";
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 return 1;
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 #getHashingDetails
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	339 sub getHashingDetails {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	340 my $self = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	341 unless(!$self->timestamph \|\| !$self->pstringh){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	342 my $programPath = cwd;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	343 $self->pstringh =~ /^(\S+)\s+(\d+)\s+(.*)$/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	344 $self->{ass_dir} = $programPath . "/" . $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	345 $self->{rmapfs} = -s $self->ass_dir . "/Roadmaps";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	346 $self->{hashval} = $2;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	347 $self->{readfilename} = $3;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	348 my @t = split /\n/, $self->velvethout;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	349 foreach(@t){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	350 if(/^(\d+).*total\.$/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	351 $self->{sequences} = $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	352 last;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	353 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	354 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	355 return 1;
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 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	358 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	359
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	360 #getAssemblyDetails
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	361 sub getAssemblyDetails {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	362 my $self = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	363 my $file = $self->ass_dir . "/contigs.fa";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	364 unless(!(-e $file)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	365
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	366 my $all = &contigStats($file,1);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	367 my $large = &contigStats($file,1000);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	368
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	369 $self->{nconts} = defined $all->{numSeqs} ? $all->{numSeqs} : 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	370 $self->{n50} = defined $all->{n50} ? $all->{n50} : 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	371 $self->{maxlength} = defined $all->{maxLen} ? $all->{maxLen} : 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	372 $self->{nconts1k} = defined $large->{numSeqs} ? $large->{numSeqs} : 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	373 $self->{totalbp} = defined $all->{numBases} ? $all->{numBases} : 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	374 $self->{totalbp1k} = defined $large->{numBases} ? $large->{numBases} : 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	375
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	376 if($self->pstringg =~ m/cov_cutoff/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	377 $self->calcAssemblyScore($self->{assmfunc2});
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 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	380 $self->calcAssemblyScore($self->{assmfunc});
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
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	383 return 1;
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 return 0;
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
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	388 #contigStats
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	389 #Original script fa-show.pl by Torsten Seemann (Monash University, Melbourne, Australia)
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	390 #Modified by Simon Gladman to suit.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	391 sub contigStats {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	392
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	393 my $file = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	394 my $minsize = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	395
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	396 print "In contigStats with $file, $minsize\n" if $interested;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	397
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	398 my $numseq=0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	399 my $avglen=0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	400 my $minlen=1E9;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	401 my $maxlen=0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	402 my @len;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	403 my $toosmall=0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	404 my $nn=0;
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 my $in = Bio::SeqIO->new(-file => $file, -format => 'Fasta');
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	407 while(my $seq = $in->next_seq()){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	408 my $L = $seq->length;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	409 #check > minsize
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	410 if($L < $minsize){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	411 $toosmall ++;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	412 next;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	413 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	414 #count Ns
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	415 my $s = $seq->seq;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	416 my $n = $s =~ s/N/N/gi;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	417 $n \|\|= 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	418 $nn += $n;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	419 #count seqs and other stats
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	420 $numseq ++;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	421 $avglen += $L;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	422 $maxlen = $L if $L > $maxlen;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	423 $minlen = $L if $L < $minlen;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	424 push @len, $L;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	425 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	426 @len = sort { $a <=> $b } @len;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	427 my $cum = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	428 my $n50 = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	429 for my $i (0 .. $#len){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	430 $cum += $len[$i];
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	431 if($cum >= $avglen/2) {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	432 $n50 = $len[$i];
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	433 last;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	434 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	435 }
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 my %out;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	438 if($numseq > 0){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	439 $out{numSeqs} = $numseq;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	440 $out{numBases} = $avglen;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	441 $out{numOK} = ($avglen - $nn);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	442 $out{numNs} = $nn;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	443 $out{minLen} = $minlen;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	444 $out{avgLen} = $avglen/$numseq;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	445 $out{maxLen} = $maxlen;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	446 $out{n50} = $n50;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	447 $out{minsize} = $minsize;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	448 $out{numTooSmall} = $toosmall;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	449 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	450 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	451 $out{$numseq} = 0;
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
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	454 print "Leaving contigstats!\n" if $interested;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	455 return (\%out);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	456 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	457
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 #toString method
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	460 sub toString {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	461 my $self = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	462 my $tmp = $self->toStringNoV();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	463 if(defined $self->velvethout){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	464 $tmp .= "Velveth Output:\n" . $self->velvethout() . "\n";
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 if(defined $self->velvetgout){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	467 $tmp .= "Velvetg Output:\n" . $self->velvetgout() . "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	468 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	469 $tmp .= "**********************************************************\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	470 return $tmp;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	471 }
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 #toStringNoV method
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	475 sub toStringNoV {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	476 my $self = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	477 my $tmp = "********************************************************\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	478 if($self->ass_id()){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	479 $tmp .= "Assembly id: " . $self->ass_id(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	480 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	481 if($self->assmscore()){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	482 $tmp .= "Assembly score: " .$self->assmscore(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	483 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	484 if($self->timestamph()){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	485 $tmp .= "Velveth timestamp: " . $self->timestamph(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	486 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	487 if($self->timestampg()){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	488 $tmp .= "Velvetg timestamp: " . $self->timestampg(). "\n";
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 if(defined $self->versionh){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	491 $tmp .= "Velveth version: " . $self->versionh(). "\n";
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 if(defined $self->versiong){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	494 $tmp .= "Velvetg version: " . $self->versiong(). "\n";
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 if(defined $self->readfilename){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	497 $tmp .= "Readfile(s): " . $self->readfilename(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	498 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	499 if(defined $self->pstringh){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	500 $tmp .= "Velveth parameter string: " . $self->pstringh(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	501 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	502 if(defined $self->pstringg){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	503 $tmp .= "Velvetg parameter string: " . $self->pstringg(). "\n";
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 if(defined $self->ass_dir){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	506 $tmp .= "Assembly directory: " . $self->ass_dir(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	507 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	508 if(defined $self->hashval){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	509 $tmp .= "Velvet hash value: " . $self->hashval(). "\n";
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 if(defined $self->rmapfs){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	512 $tmp .= "Roadmap file size: " . $self->rmapfs(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	513 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	514 if(defined $self->sequences){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	515 $tmp .= "Total number of sequences: " . $self->sequences(). "\n";
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 if(defined $self->nconts){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	518 $tmp .= "Total number of contigs: " . $self->nconts(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	519 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	520 if(defined $self->n50){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	521 $tmp .= "n50: " . $self->n50(). "\n";
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 if(defined $self->maxlength){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	524 $tmp .= "length of longest contig: " . $self->maxlength(). "\n";
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 if(defined $self->totalbp){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	527 $tmp .= "Total bases in contigs: " . $self->totalbp(). "\n";
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 if(defined $self->nconts1k){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	530 $tmp .= "Number of contigs > 1k: " . $self->nconts1k(). "\n";
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 if(defined $self->totalbp1k){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	533 $tmp .= "Total bases in contigs > 1k: " . $self->totalbp1k(). "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	534 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	535 if($self->pstringh =~ /Pair/ && defined $self->pstringg && $self->pstringg =~ /-exp_cov/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	536 $tmp .= "Paired Library insert stats:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	537 my @x = split /\n/, $self->velvetgout;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	538 foreach(@x){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	539 chomp;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	540 if(/^Paired-end library \d+ has/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	541 $tmp .= "$_\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	542 }
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 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	545 $tmp .= "**********************************************************\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	546 return $tmp;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	547 }
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 sub opt_func_toString {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	550 my $out = "\nVelvet optimiser assembly optimisation function can be built from the following variables.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	551 foreach my $key (sort keys %f_opts){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	552 $out .= "\t$key = " . $f_opts{$key}->{'desc'} . "\n";
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 $out .= "Examples are:\n\t'Lbp' = Just the total basepairs in contigs longer than 1kb\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	555 $out .= "\t'n50*Lcon' = The n50 times the number of long contigs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	556 $out .= "\t'n50*Lcon/tbp+log(Lbp)' = The n50 times the number of long contigs divided\n\t\tby the total bases in all contigs plus the log of the number of bases\n\t\tin long contigs.\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	557 return $out
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	558 }
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 1;

Mercurial > repos > konradpaszkiewicz > velvetoptimiser

annotate VelvetOptimiser-2.1.7_modified/VelvetOpt/Assembly.pm @ 0:7363fee7f20c default tip