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

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

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

author	konradpaszkiewicz
date	Tue, 07 Jun 2011 17:42:26 -0400
parents
children

rev	line source
0 7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 # VelvetOpt::hwrap.pm
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	3 # Copyright 2008 Simon Gladman <simon.gladman@csiro.au>
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5 # This program is free software; you can redistribute it and/or modify
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	6 # it under the terms of the GNU General Public License as published by
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	7 # the Free Software Foundation; either version 2 of the License, or
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	8 # (at your option) any later version.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 # This program is distributed in the hope that it will be useful,
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	13 # GNU General Public License for more details.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 # You should have received a copy of the GNU General Public License
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	16 # along with this program; if not, write to the Free Software
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	18 # MA 02110-1301, USA.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	19 #
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	20 # Version 1.1 - 14/07/2010 - Added support for changing input file types
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 # Version 1.2 - 11/08/2010 - Changed velveth help parser for new velvet help format
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	22 # Thanks to Alexie Papanicolaou - CSIRO for the patch.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	23
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24 package VelvetOpt::hwrap;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	25
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	26 =head1 NAME
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	28 VelvetOpt::hwrap.pm - Velvet hashing program wrapper module.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	29
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	30 =head1 AUTHOR
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	31
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	32 Simon Gladman, CSIRO, 2007, 2008.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	33
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	34 =head1 LICENSE
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	35
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	36 Copyright 2008 Simon Gladman <simon.gladman@csiro.au>
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	37
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	38 This program is free software; you can redistribute it and/or modify
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	39 it under the terms of the GNU General Public License as published by
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	40 the Free Software Foundation; either version 2 of the License, or
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	41 (at your option) any later version.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	42
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	43 This program is distributed in the hope that it will be useful,
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	44 but WITHOUT ANY WARRANTY; without even the implied warranty of
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	45 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	46 GNU General Public License for more details.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	47
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	48 You should have received a copy of the GNU General Public License
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	49 along with this program; if not, write to the Free Software
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	50 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	51 MA 02110-1301, USA.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	52
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	53 =head1 SYNOPSIS
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	54
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	55 use VelvetOpt::hwrap;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	56 use VelvetOpt::Assembly;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	57 my $object = VelvetOpt::Assembly->new(
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	58 timestamph => "23 November 2008 15:00:00",
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	59 ass_id => "1",
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	60 versionh => "0.7.04",
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	61 pstringh => "test 21 -fasta test_reads.fna",
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	62 ass_dir => "/home/gla048/Desktop/newVelvetOptimiser/data_1"
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	63 );
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	64 my $worked = VelvetOpt::hwrap::objectVelveth($object);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	65 if($worked){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	66 print $object->toString();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	67 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	68 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	69 die "Error in velveth..\n" . $object->toString();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	70 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	71
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	72 =head1 DESCRIPTION
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	73
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	74 A wrapper module to run velveth on VelvetAssembly objects or on velveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	75 parameter strings. Also contains private methods to check velveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	76 parameter strings, run velveth and return results.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	77
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	78 =head2 Uses
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	79
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	80 =over 8
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	81
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	82 =item strict
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	83
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	84 =item warnings
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	85
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	86 =item Carp
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	87
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	88 =item VelvetOpt::Assembly
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	89
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	90 =item POSIX qw(strftime)
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	91
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	92 =back
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	93
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	94 =head2 Private Fields
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	95
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	96 =over 8
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	97
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	98 =item interested
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	99
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	100 STDERR printing debug message toggle. 1 for on, 0 for off.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	101
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	102 =back
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	103
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	104 =head2 Methods
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	105
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	106 =over 8
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	107
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	108 =item _runVelveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	109
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	110 Private method which runs velveth with the supplied velveth parameter string and returns velveth output messages as a string.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	111
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	112 =item _checkVHString
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	113
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	114 Private method which checks for a correctly formatted velveth string. Returns 1 or 0.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	115
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	116 =item objectVelveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	117
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	118 Accepts a VelvetAssembly object and the number of categories velvet was compiled with, looks for the velveth parameter string it contains, checks it, sends it to _runVelveth, collects the results and stores them in the VelvetAssembly object.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	119
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	120 =item stringVelveth
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	121
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	122 Accepts a velveth parameter string and the number of categories velvet was compiled with, checks it, sends it to _runVelveth and then collects and returns the velveth output messages.
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	123
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	124 =back
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	125
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	126 =cut
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	127
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	128 use warnings;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	129 use strict;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	130 use Carp;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	131 use VelvetOpt::Assembly;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	132 use POSIX qw(strftime);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	133
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	134 my $interested = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	135
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	136 my @Fileformats;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	137 my @Readtypes;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	138 my $usage;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	139 my $inited = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	140
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	141 sub init {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	142 #run a velveth to get its help lines..
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	143 my $response = &_runVelveth(" ");
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	144
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	145 $response =~ m/CATEGORIES = (\d+)/;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	146 my $cats = $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	147 unless($cats){$cats = 2;}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	148
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	149 $response =~ m/(File format options:(.*)Read type options)/s;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	150 my @t = split /\n/, $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	151 foreach(@t){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	152 #if(/\s+(-\S+)/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	153 while(/\s+(-\S+)/g){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	154 push @Fileformats, $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	155 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	156 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	157
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	158 $response =~ m/(Read type options:(.*)Options:)/s;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	159
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	160 @t = ();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	161 @t = split /\n/, $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	162 foreach(@t){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	163 #if(/\s+(-\S+)/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	164 while(/\s+(-\S+)/g){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	165 push @Readtypes, $1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	166 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	167 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	168
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	169 for(my $i = 3; $i <= $cats; $i++){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	170 push @Readtypes, "-short$i";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	171 push @Readtypes, "-shortPaired$i";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	172 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	173
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	174 $usage = "Incorrect velveth parameter string: Needs to be of the form\n{[-file_format][-read_type] filename}\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	175 $usage .= "Where:\n\tFile format options:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	176 foreach(@Fileformats){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	177 $usage .= "\t$_\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	178 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	179 $usage .= "Read type options:\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	180 foreach(@Readtypes){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	181 $usage .= "\t$_\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	182 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	183 $usage .= "\nThere can be more than one filename specified as long as its a different type.\nStopping run\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	184
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	185 $inited = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	186 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	187
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	188 sub _runVelveth {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	189 #unless($inited){ &init(); }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	190 my $cmdline = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	191 my $output = "";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	192 print STDERR "About to run velveth!\n" if $interested;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	193 $output = `velveth $cmdline`;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	194 $output .= "\nTimestamp: " . strftime("%b %e %Y %H:%M:%S", localtime) . "\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	195 return $output;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	196 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	197
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	198 sub _checkVHString {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	199 unless($inited){ &init(); }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	200 my $line = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	201 my $cats = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	202
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	203
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	204
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	205 my %fileform = ();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	206 my %readform = ();
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	207
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	208 foreach(@Fileformats){ $fileform{$_} = 1;}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	209 foreach(@Readtypes){ $readform{$_} = 1;}
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	210
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	211 my @l = split /\s+/, $line;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	212
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	213 #first check for a directory name as the first parameter...
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	214 my $dir = shift @l;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	215 if(!($dir =~ /\w+/) \|\| ($dir =~ /^\-/)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	216 carp "**** $line\n\tNo directory name specified as first parameter in velveth string. Internal error!\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	217 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	218 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	219 #print "VH Check passed directory..\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	220 my $hash = shift @l;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	221 unless($hash =~ /^\d+$/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	222 carp "**** $line\n\tHash value in velveth string not a number. Internal error!\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	223 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	224 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	225
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	226 #print "VH check passed hash value..\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	227
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	228 my $i = 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	229 my $ok = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	230 foreach(@l){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	231 if(/^-/){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	232 #s/-//;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	233 if(!$fileform{$_} && !$readform{$_}){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	234 carp "**** $line\n\tIncorrect fileformat or readformat specified.\n\t$_ is an invalid velveth switch.\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	235 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	236 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	237 elsif($fileform{$_}){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	238 if(($i + 1) > $#l){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	239 carp "$line\n\tNo filename supplied after file format type $l[$i].\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	240 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	241 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	242 if($readform{$l[$i+1]}){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	243 if(($i+2) > $#l){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	244 carp "$line\n\tNo filename supplied after read format type $l[$i+1].\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	245 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	246 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	247 if(-e $l[$i+2]){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	248 $ok = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	249 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	250 else{
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	251 carp "**** $line\n\tVelveth filename " . $l[$i+2] . " doesn't exist.\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	252 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	253 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	254 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	255 elsif (-e $l[$i+1]){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	256 $ok = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	257 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	258 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	259 carp "**** $line\n\tVelveth filename " . $l[$i+1] . " doesn't exist.$usage\n";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	260 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	261 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	262 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	263 elsif($readform{$_}){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	264 if(($i + 1) > $#l){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	265 carp "$line\n\tNo filename supplied after read format type $l[$i].\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	266 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	267 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	268 if($fileform{$l[$i+1]}){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	269 if(($i+2) > $#l){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	270 carp "$line\n\tNo filename supplied after file format type $l[$i+1].\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	271 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	272 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	273 if(-e $l[$i+2]){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	274 $ok = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	275 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	276 else{
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	277 carp "**** $line\n\tVelveth filename " . $l[$i+2] . " doesn't exist.\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	278 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	279 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	280 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	281 elsif (-e $l[$i+1]){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	282 $ok = 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	283 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	284 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	285 carp "**** $line\n\tVelveth filename " . $l[$i+1] ." doesn't exist.\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	286 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	287 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	288 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	289 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	290 elsif(!-e $_){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	291 carp "**** $line\n\tVelveth filename $_ doesn't exist.\n$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	292 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	293 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	294 $i ++;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	295 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	296 if($ok){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	297 return 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	298 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	299 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	300
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	301 sub objectVelveth {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	302 unless($inited){ &init(); }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	303 my $va = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	304 my $cats = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	305 my $cmdline = $va->{pstringh};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	306 if(_checkVHString($cmdline, $cats)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	307 $va->{velvethout} = _runVelveth($cmdline);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	308 my @t = split /\n/, $va->{velvethout};
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	309 $t[$#t] =~ s/Timestamp:\s+//;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	310 $va->{timestamph} = $t[$#t];
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	311 return 1;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	312 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	313 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	314 $va->{velvethout} = "Formatting errors in velveth parameter string.$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	315 return 0;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	316 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	317 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	318
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	319 sub stringVelveth {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	320 unless($inited){ &init(); }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	321 my $cmdline = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	322 my $cats = shift;
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	323 if(_checkVHString($cmdline,$cats)){
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	324 return _runVelveth($cmdline);
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	325 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	326 else {
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	327 return "Formatting errors in velveth parameter string.$usage";
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	328 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	329 }
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	330
7363fee7f20c Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	331 1;

Mercurial > repos > konradpaszkiewicz > velvetoptimiser

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