Mercurial > repos > konradpaszkiewicz > velvetoptimiser
annotate VelvetOptimiser-2.1.7_modified/VelvetOpt/hwrap.pm @ 0:50ae1360fbbe default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 18:07:56 -0400 |
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1 # VelvetOpt::hwrap.pm |
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2 # |
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3 # Copyright 2008 Simon Gladman <simon.gladman@csiro.au> |
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4 # |
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5 # This program is free software; you can redistribute it and/or modify |
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6 # it under the terms of the GNU General Public License as published by |
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7 # the Free Software Foundation; either version 2 of the License, or |
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8 # (at your option) any later version. |
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9 # |
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10 # This program is distributed in the hope that it will be useful, |
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of |
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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13 # GNU General Public License for more details. |
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14 # |
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15 # You should have received a copy of the GNU General Public License |
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16 # along with this program; if not, write to the Free Software |
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17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, |
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18 # MA 02110-1301, USA. |
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19 # |
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20 # Version 1.1 - 14/07/2010 - Added support for changing input file types |
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21 # Version 1.2 - 11/08/2010 - Changed velveth help parser for new velvet help format |
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22 # Thanks to Alexie Papanicolaou - CSIRO for the patch. |
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23 |
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24 package VelvetOpt::hwrap; |
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25 |
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26 =head1 NAME |
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27 |
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28 VelvetOpt::hwrap.pm - Velvet hashing program wrapper module. |
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29 |
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30 =head1 AUTHOR |
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31 |
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32 Simon Gladman, CSIRO, 2007, 2008. |
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33 |
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34 =head1 LICENSE |
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35 |
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36 Copyright 2008 Simon Gladman <simon.gladman@csiro.au> |
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37 |
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38 This program is free software; you can redistribute it and/or modify |
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39 it under the terms of the GNU General Public License as published by |
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40 the Free Software Foundation; either version 2 of the License, or |
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41 (at your option) any later version. |
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42 |
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43 This program is distributed in the hope that it will be useful, |
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44 but WITHOUT ANY WARRANTY; without even the implied warranty of |
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45 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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46 GNU General Public License for more details. |
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47 |
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48 You should have received a copy of the GNU General Public License |
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49 along with this program; if not, write to the Free Software |
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50 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, |
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51 MA 02110-1301, USA. |
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52 |
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53 =head1 SYNOPSIS |
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54 |
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55 use VelvetOpt::hwrap; |
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56 use VelvetOpt::Assembly; |
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57 my $object = VelvetOpt::Assembly->new( |
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58 timestamph => "23 November 2008 15:00:00", |
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59 ass_id => "1", |
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60 versionh => "0.7.04", |
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61 pstringh => "test 21 -fasta test_reads.fna", |
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62 ass_dir => "/home/gla048/Desktop/newVelvetOptimiser/data_1" |
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63 ); |
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64 my $worked = VelvetOpt::hwrap::objectVelveth($object); |
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65 if($worked){ |
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66 print $object->toString(); |
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67 } |
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68 else { |
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69 die "Error in velveth..\n" . $object->toString(); |
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70 } |
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71 |
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72 =head1 DESCRIPTION |
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73 |
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74 A wrapper module to run velveth on VelvetAssembly objects or on velveth |
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75 parameter strings. Also contains private methods to check velveth |
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76 parameter strings, run velveth and return results. |
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77 |
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78 =head2 Uses |
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79 |
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80 =over 8 |
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81 |
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82 =item strict |
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83 |
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84 =item warnings |
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85 |
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86 =item Carp |
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87 |
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88 =item VelvetOpt::Assembly |
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89 |
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90 =item POSIX qw(strftime) |
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91 |
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92 =back |
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93 |
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94 =head2 Private Fields |
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95 |
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96 =over 8 |
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97 |
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98 =item interested |
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99 |
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100 STDERR printing debug message toggle. 1 for on, 0 for off. |
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101 |
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102 =back |
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103 |
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104 =head2 Methods |
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105 |
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106 =over 8 |
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107 |
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108 =item _runVelveth |
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109 |
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110 Private method which runs velveth with the supplied velveth parameter string and returns velveth output messages as a string. |
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111 |
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112 =item _checkVHString |
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113 |
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114 Private method which checks for a correctly formatted velveth string. Returns 1 or 0. |
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115 |
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116 =item objectVelveth |
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117 |
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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. |
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119 |
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120 =item stringVelveth |
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121 |
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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. |
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123 |
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124 =back |
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125 |
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126 =cut |
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127 |
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128 use warnings; |
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129 use strict; |
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130 use Carp; |
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131 use VelvetOpt::Assembly; |
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132 use POSIX qw(strftime); |
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133 |
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134 my $interested = 0; |
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135 |
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136 my @Fileformats; |
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137 my @Readtypes; |
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138 my $usage; |
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139 my $inited = 0; |
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140 |
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141 sub init { |
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142 #run a velveth to get its help lines.. |
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143 my $response = &_runVelveth(" "); |
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144 |
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145 $response =~ m/CATEGORIES = (\d+)/; |
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146 my $cats = $1; |
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147 unless($cats){$cats = 2;} |
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148 |
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149 $response =~ m/(File format options:(.*)Read type options)/s; |
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150 my @t = split /\n/, $1; |
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151 foreach(@t){ |
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152 #if(/\s+(-\S+)/){ |
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153 while(/\s+(-\S+)/g){ |
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154 push @Fileformats, $1; |
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155 } |
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156 } |
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157 |
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158 $response =~ m/(Read type options:(.*)Options:)/s; |
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159 |
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160 @t = (); |
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161 @t = split /\n/, $1; |
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162 foreach(@t){ |
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163 #if(/\s+(-\S+)/){ |
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164 while(/\s+(-\S+)/g){ |
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165 push @Readtypes, $1; |
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166 } |
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167 } |
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168 |
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169 for(my $i = 3; $i <= $cats; $i++){ |
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170 push @Readtypes, "-short$i"; |
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171 push @Readtypes, "-shortPaired$i"; |
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172 } |
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173 |
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174 $usage = "Incorrect velveth parameter string: Needs to be of the form\n{[-file_format][-read_type] filename}\n"; |
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175 $usage .= "Where:\n\tFile format options:\n"; |
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176 foreach(@Fileformats){ |
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177 $usage .= "\t$_\n"; |
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178 } |
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179 $usage .= "Read type options:\n"; |
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180 foreach(@Readtypes){ |
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181 $usage .= "\t$_\n"; |
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182 } |
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183 $usage .= "\nThere can be more than one filename specified as long as its a different type.\nStopping run\n"; |
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184 |
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185 $inited = 1; |
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186 } |
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187 |
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188 sub _runVelveth { |
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189 #unless($inited){ &init(); } |
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190 my $cmdline = shift; |
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191 my $output = ""; |
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192 print STDERR "About to run velveth!\n" if $interested; |
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193 $output = `velveth $cmdline`; |
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194 $output .= "\nTimestamp: " . strftime("%b %e %Y %H:%M:%S", localtime) . "\n"; |
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195 return $output; |
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196 } |
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197 |
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198 sub _checkVHString { |
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199 unless($inited){ &init(); } |
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200 my $line = shift; |
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201 my $cats = shift; |
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202 |
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203 |
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204 |
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205 my %fileform = (); |
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206 my %readform = (); |
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207 |
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208 foreach(@Fileformats){ $fileform{$_} = 1;} |
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209 foreach(@Readtypes){ $readform{$_} = 1;} |
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210 |
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211 my @l = split /\s+/, $line; |
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212 |
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213 #first check for a directory name as the first parameter... |
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214 my $dir = shift @l; |
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215 if(!($dir =~ /\w+/) || ($dir =~ /^\-/)){ |
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216 carp "**** $line\n\tNo directory name specified as first parameter in velveth string. Internal error!\n$usage"; |
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217 return 0; |
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218 } |
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219 #print "VH Check passed directory..\n"; |
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220 my $hash = shift @l; |
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221 unless($hash =~ /^\d+$/){ |
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222 carp "**** $line\n\tHash value in velveth string not a number. Internal error!\n$usage"; |
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223 return 0; |
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224 } |
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225 |
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226 #print "VH check passed hash value..\n"; |
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227 |
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228 my $i = 0; |
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229 my $ok = 1; |
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230 foreach(@l){ |
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231 if(/^-/){ |
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232 #s/-//; |
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233 if(!$fileform{$_} && !$readform{$_}){ |
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234 carp "**** $line\n\tIncorrect fileformat or readformat specified.\n\t$_ is an invalid velveth switch.\n$usage"; |
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235 return 0; |
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236 } |
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237 elsif($fileform{$_}){ |
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238 if(($i + 1) > $#l){ |
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239 carp "$line\n\tNo filename supplied after file format type $l[$i].\n$usage"; |
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240 return 0; |
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241 } |
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242 if($readform{$l[$i+1]}){ |
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243 if(($i+2) > $#l){ |
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244 carp "$line\n\tNo filename supplied after read format type $l[$i+1].\n$usage"; |
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245 return 0; |
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246 } |
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247 if(-e $l[$i+2]){ |
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248 $ok = 1; |
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249 } |
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250 else{ |
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251 carp "**** $line\n\tVelveth filename " . $l[$i+2] . " doesn't exist.\n$usage"; |
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252 return 0; |
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253 } |
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254 } |
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255 elsif (-e $l[$i+1]){ |
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256 $ok = 1; |
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257 } |
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258 else { |
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259 carp "**** $line\n\tVelveth filename " . $l[$i+1] . " doesn't exist.$usage\n"; |
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260 return 0; |
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261 } |
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262 } |
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263 elsif($readform{$_}){ |
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264 if(($i + 1) > $#l){ |
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265 carp "$line\n\tNo filename supplied after read format type $l[$i].\n$usage"; |
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266 return 0; |
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267 } |
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268 if($fileform{$l[$i+1]}){ |
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269 if(($i+2) > $#l){ |
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270 carp "$line\n\tNo filename supplied after file format type $l[$i+1].\n$usage"; |
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271 return 0; |
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272 } |
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273 if(-e $l[$i+2]){ |
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274 $ok = 1; |
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275 } |
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276 else{ |
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277 carp "**** $line\n\tVelveth filename " . $l[$i+2] . " doesn't exist.\n$usage"; |
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278 return 0; |
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279 } |
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280 } |
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281 elsif (-e $l[$i+1]){ |
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282 $ok = 1; |
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283 } |
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284 else { |
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285 carp "**** $line\n\tVelveth filename " . $l[$i+1] ." doesn't exist.\n$usage"; |
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286 return 0; |
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287 } |
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288 } |
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289 } |
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290 elsif(!-e $_){ |
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291 carp "**** $line\n\tVelveth filename $_ doesn't exist.\n$usage"; |
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292 return 0; |
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293 } |
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294 $i ++; |
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295 } |
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296 if($ok){ |
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297 return 1; |
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298 } |
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299 } |
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300 |
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301 sub objectVelveth { |
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302 unless($inited){ &init(); } |
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303 my $va = shift; |
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304 my $cats = shift; |
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305 my $cmdline = $va->{pstringh}; |
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306 if(_checkVHString($cmdline, $cats)){ |
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307 $va->{velvethout} = _runVelveth($cmdline); |
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308 my @t = split /\n/, $va->{velvethout}; |
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309 $t[$#t] =~ s/Timestamp:\s+//; |
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310 $va->{timestamph} = $t[$#t]; |
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311 return 1; |
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312 } |
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313 else { |
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314 $va->{velvethout} = "Formatting errors in velveth parameter string.$usage"; |
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315 return 0; |
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316 } |
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317 } |
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318 |
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319 sub stringVelveth { |
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320 unless($inited){ &init(); } |
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321 my $cmdline = shift; |
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322 my $cats = shift; |
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323 if(_checkVHString($cmdline,$cats)){ |
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324 return _runVelveth($cmdline); |
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325 } |
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326 else { |
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327 return "Formatting errors in velveth parameter string.$usage"; |
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328 } |
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329 } |
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330 |
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331 1; |