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

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

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

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

rev	line source
0 50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 # VelvetOpt::Assembly.pm
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 #
50ae1360fbbe 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>
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4 #
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9 #
50ae1360fbbe 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,
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14 #
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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,
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	19
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 #
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24 #
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27 #
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	30 #
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	33 #
50ae1360fbbe 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
50ae1360fbbe 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).
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	36
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	37 package VelvetOpt::Assembly;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	38
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	39 =head1 NAME
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	40
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	42
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	43 =head1 AUTHOR
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	44
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	46
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	47 =head1 LICENSE
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	48
50ae1360fbbe 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>
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	50
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	55
50ae1360fbbe 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,
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	60
50ae1360fbbe 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
50ae1360fbbe 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
50ae1360fbbe 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,
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	65
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	66 =head1 SYNOPSIS
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	67
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	68 use VelvetOpt::Assembly;
50ae1360fbbe 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(
50ae1360fbbe 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",
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	71 ass_id => "1",
50ae1360fbbe 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",
50ae1360fbbe 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"
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	74 );
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	75 print $object->toString();
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	76
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	77 =head1 DESCRIPTION
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	78
50ae1360fbbe 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,
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	81
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	82 Version 1.1
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	83
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	84 =head2 Uses
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	85
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	86 =over 8
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	87
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	88 =item strict
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	89
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	90 =item warnings
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	91
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	92 =item Carp
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	93
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	94 =back
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	95
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	96 =head2 Fields
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	97
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	98 =over 8
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	99
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	100 =item assmscore
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	101
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	103
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	104 =item timstamph
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	105
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	107
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	108 =item timestampg
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	109
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	111
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	112 =item ass_id
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	113
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	115
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	116 =item versionh
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	117
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	119
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	120 =item versiong
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	121
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	123
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	124 =item readfilename
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	125
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	126 The name of the file containing all the reads (or a qw of them if more than one...)
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	127
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	128 =item pstringh
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	129
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	130 The velveth parameter string used in this assembly
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	131
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	132 =item pstringg
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	133
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	135
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	136 =item ass_dir
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	137
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	138 The assembly directory path (full)
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	139
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	140 =item hashval
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	141
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	143
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	144 =item rmapfs
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	145
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	147
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	148 =item sequences
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	149
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	150 The total number of sequences in the input files
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	151
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	152 =item nconts
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	153
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	154 The number of contigs in the final assembly
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	155
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	156 =item totalbp
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	157
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	159
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	160 =item n50
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	161
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	163
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	164 =item maxlength
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	165
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	167
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	168 =item maxcont
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	169
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	170 The size of the largest contig in the assembly
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	171
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	172 =item nconts1k
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	173
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	174 The number of contigs greater than 1k in size
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	175
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	176 =item totalbp1k
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	177
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	179
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	180 =item velvethout
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	181
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	182 The velveth output
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	183
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	184 =item velvetgout
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	185
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	186 The velvetg output
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	187
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	188 =back
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	189
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	190 =head2 Methods
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	191
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	192 =over 8
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	193
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	194 =item new
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	195
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	197
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	198 =item accessor methods
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	199
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	200 Accessor methods for all fields.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	201
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	202 =item calcAssemblyScore
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	203
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	205
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	206 =item getHashingDetails
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	207
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	208 Gets the details of the outputs from the velveth run and stores it in self.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	209
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	210 =item getAssemblyDetails
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	211
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	213
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	214 =item toString
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	215
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	216 Returns a string representation of the object's contents.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	217
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	218 =item toStringNoV
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	219
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	221
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	223
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	225
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	226 =back
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	227
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	228 =cut
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	229
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	230 use strict;
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	232 use Carp;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	233 use warnings;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	234 #use base "Storable";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	235 use Cwd;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	236 use Bio::SeqIO;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	237
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	238 my $interested = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	239
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	240
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	241
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	242 #constructor
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	243 sub new {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	244 my $class = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	245 my $self = {@_};
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	246 bless ($self, $class);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	247 return $self;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	248 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	249
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	250 #optimisation function options...
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	251 my %f_opts;
50ae1360fbbe 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';
50ae1360fbbe 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";
50ae1360fbbe 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';
50ae1360fbbe 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";
50ae1360fbbe 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';
50ae1360fbbe 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";
50ae1360fbbe 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';
50ae1360fbbe 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";
50ae1360fbbe 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';
50ae1360fbbe 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";
50ae1360fbbe 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';
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	264
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	265 #accessor methods
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe 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}}
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	289
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	290 #assemblyScoreCalculator
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	291 sub calcAssemblyScore {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	292 use Safe;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	293
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	294 my $self = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	295 my $func = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	296
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	298
50ae1360fbbe 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
50ae1360fbbe 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));
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	301 #Comparators
50ae1360fbbe 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));
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	303 #Base math
50ae1360fbbe 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));
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	305 #Binary math
50ae1360fbbe 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));
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	307 #Regex
50ae1360fbbe 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));
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	309 #Conditionals
50ae1360fbbe 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));
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	311 #Advanced math
50ae1360fbbe 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));
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	313
50ae1360fbbe 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){
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	316
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	318 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	319
50ae1360fbbe 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);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	321 warn $@ if $@;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	322 $self->{assmscore} = $r;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	323 unless($r =~ /^\d+/){
50ae1360fbbe 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";
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	326 $self->{assmscore} = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	327 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	328 if($r == 0){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	329 print STDERR "**********\n";
50ae1360fbbe 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";
50ae1360fbbe 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";
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	333 print STDERR "**********\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	334 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	335 return 1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	336 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	337
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	338 #getHashingDetails
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	339 sub getHashingDetails {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	340 my $self = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	341 unless(!$self->timestamph \|\| !$self->pstringh){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	342 my $programPath = cwd;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	343 $self->pstringh =~ /^(\S+)\s+(\d+)\s+(.*)$/;
50ae1360fbbe 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;
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	346 $self->{hashval} = $2;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	347 $self->{readfilename} = $3;
50ae1360fbbe 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/, $self->velvethout;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	349 foreach(@t){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	350 if(/^(\d+).*total\.$/){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	351 $self->{sequences} = $1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	352 last;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	353 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	354 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	355 return 1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	356 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	357 return 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	358 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	359
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	360 #getAssemblyDetails
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	361 sub getAssemblyDetails {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	362 my $self = shift;
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	364 unless(!(-e $file)){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	365
50ae1360fbbe 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);
50ae1360fbbe 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);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	368
50ae1360fbbe 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;
50ae1360fbbe 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;
50ae1360fbbe 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;
50ae1360fbbe 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;
50ae1360fbbe 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;
50ae1360fbbe 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} ? $large->{numBases} : 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	375
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	376 if($self->pstringg =~ m/cov_cutoff/){
50ae1360fbbe 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});
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	378 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	379 else {
50ae1360fbbe 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});
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	381 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	382
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	383 return 1;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	384 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	385 return 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	386 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	387
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	388 #contigStats
50ae1360fbbe 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)
50ae1360fbbe 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.
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	391 sub contigStats {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	392
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	393 my $file = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	394 my $minsize = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	395
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	397
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	398 my $numseq=0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	399 my $avglen=0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	400 my $minlen=1E9;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	401 my $maxlen=0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	402 my @len;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	403 my $toosmall=0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	404 my $nn=0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	405
50ae1360fbbe 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');
50ae1360fbbe 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()){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	408 my $L = $seq->length;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	409 #check > minsize
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	410 if($L < $minsize){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	411 $toosmall ++;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	412 next;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	413 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	414 #count Ns
50ae1360fbbe 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;
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	417 $n \|\|= 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	418 $nn += $n;
50ae1360fbbe 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
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	420 $numseq ++;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	421 $avglen += $L;
50ae1360fbbe 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;
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	424 push @len, $L;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	425 }
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	427 my $cum = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	428 my $n50 = 0;
50ae1360fbbe 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){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	430 $cum += $len[$i];
50ae1360fbbe 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) {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	432 $n50 = $len[$i];
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	433 last;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	434 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	435 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	436
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	437 my %out;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	438 if($numseq > 0){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	439 $out{numSeqs} = $numseq;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	440 $out{numBases} = $avglen;
50ae1360fbbe 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);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	442 $out{numNs} = $nn;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	443 $out{minLen} = $minlen;
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	445 $out{maxLen} = $maxlen;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	446 $out{n50} = $n50;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	447 $out{minsize} = $minsize;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	448 $out{numTooSmall} = $toosmall;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	449 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	450 else {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	451 $out{$numseq} = 0;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	452 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	453
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	455 return (\%out);
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	456 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	457
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	458
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	459 #toString method
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	460 sub toString {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	461 my $self = shift;
50ae1360fbbe 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();
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	465 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	468 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	469 $tmp .= "**********************************************************\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	470 return $tmp;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	471 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	472
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	473
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	474 #toStringNoV method
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	475 sub toStringNoV {
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	476 my $self = shift;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	477 my $tmp = "********************************************************\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	478 if($self->ass_id()){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	479 $tmp .= "Assembly id: " . $self->ass_id(). "\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	480 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	481 if($self->assmscore()){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	483 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	484 if($self->timestamph()){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	485 $tmp .= "Velveth timestamp: " . $self->timestamph(). "\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	486 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	487 if($self->timestampg()){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	489 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	492 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	495 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	498 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	501 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	504 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	507 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	510 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	513 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	516 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	519 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	522 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	525 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	528 }
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	531 }
50ae1360fbbe 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){
50ae1360fbbe 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: " . $self->totalbp1k(). "\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	534 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	535 if($self->pstringh =~ /Pair/ && defined $self->pstringg && $self->pstringg =~ /-exp_cov/){
50ae1360fbbe 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";
50ae1360fbbe 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;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	538 foreach(@x){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	539 chomp;
50ae1360fbbe 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/){
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	541 $tmp .= "$_\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	542 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	543 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	544 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	545 $tmp .= "**********************************************************\n";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	546 return $tmp;
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	547 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	548
50ae1360fbbe 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 {
50ae1360fbbe 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";
50ae1360fbbe 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){
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	553 }
50ae1360fbbe 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";
50ae1360fbbe 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";
50ae1360fbbe 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";
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	557 return $out
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	558 }
50ae1360fbbe Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	559
50ae1360fbbe 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 @ 0:50ae1360fbbe default tip