Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/ReMatCh/utils/restart_rematch.py @ 0:965517909457 draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 08:41:44 -0500
parents
children 0cbed1c0a762
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0
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1 #!/usr/bin/env python
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2
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3 # -*- coding: utf-8 -*-
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4
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5 """
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6 restart_rematch.py - Restarts a ReMatCh run abruptly terminated
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7 <https://github.com/B-UMMI/ReMatCh/>
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8
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9 Copyright (C) 2017 Miguel Machado <mpmachado@medicina.ulisboa.pt>
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10
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11 Last modified: February 09, 2017
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12
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13 This program is free software: you can redistribute it and/or modify
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14 it under the terms of the GNU General Public License as published by
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15 the Free Software Foundation, either version 3 of the License, or
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16 (at your option) any later version.
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17
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18 This program is distributed in the hope that it will be useful,
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19 but WITHOUT ANY WARRANTY; without even the implied warranty of
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20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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21 GNU General Public License for more details.
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22
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23 You should have received a copy of the GNU General Public License
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24 along with this program. If not, see <http://www.gnu.org/licenses/>.
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25 """
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26
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27 import os
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28 import argparse
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29 import subprocess
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30 import time
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31
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32
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33 version = '0.1'
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34
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35
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36 def runRematch(args):
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37 print '\n' + '==========> Restarting ReMatCh <==========' + '\n'
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38
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39 workdir = os.path.abspath(args.workdir)
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40 if not os.path.isdir(workdir):
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41 os.makedirs(workdir)
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42
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43 initialWorkdir = os.path.abspath(args.initialWorkdir)
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44
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45 files_required = get_files_required(initialWorkdir)
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46
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47 samples_run = get_samples_run(files_required['sample_report']['file'])
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48
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49 command, list_ids, taxon, threads, initial_present_directory = get_rematch_command(files_required['run']['file'])
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50
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51 if list_ids is not None:
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52 total_samples = getListIDs_fromFile(list_ids)
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53 elif taxon:
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54 total_samples = getTaxonRunIDs(files_required['IDs_list.seqFromWebTaxon']['file'])
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55 else:
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56 samples_fastq = searchFastqFiles(initialWorkdir)
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57 total_samples = samples_fastq.keys()
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58
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59 samples_to_run = list(set(total_samples).symmetric_difference(set(sum(samples_run.values(), []) if not args.runFailedSamples else samples_run['True'] if 'True' in samples_run else [''])))
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60
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61 print str(len(samples_to_run)) + ' samples out of ' + str(len(total_samples)) + ' will be analysed by ReMatCh' + '\n'
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62
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63 if list_ids is not None or taxon:
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64 samples_to_run_file = write_samples_to_run(samples_to_run, workdir)
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65 else:
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66 setSamples_fromFolders(samples_to_run, samples_fastq, workdir)
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67
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68 command.extend(['-w', workdir])
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69 command.extend(['-j', str(threads) if args.threads is None else str(args.threads)])
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70 if list_ids is not None or taxon:
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71 command.extend(['-l', samples_to_run_file])
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72
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73 print 'ReMatCh will start in 5 seconds...'
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74 time.sleep(5)
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75
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76 os.chdir(initial_present_directory)
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77 subprocess.call(command)
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78
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79
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80 def write_samples_to_run(samples_to_run, workdir):
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81 samples_to_run_file = os.path.join(workdir, 'restart_rematch.samples_to_run.txt')
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82 with open(samples_to_run_file, 'wt') as writer:
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83 for sample in samples_to_run:
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84 writer.write(sample + '\n')
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85 return samples_to_run_file
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86
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87
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88 def get_files_required(initialWorkdir):
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89 files_required = {'sample_report': {'extension': 'tab'}, 'run': {'extension': 'log'}, 'IDs_list.seqFromWebTaxon': {'extension': 'tab'}}
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90 files = sorted([f for f in os.listdir(initialWorkdir) if not f.startswith('.') and os.path.isfile(os.path.join(initialWorkdir, f))])
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91 for file_found in files:
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92 file_path = os.path.join(initialWorkdir, file_found)
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93 file_modification = os.path.getmtime(file_path)
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94 for prefix, values in files_required.items():
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95 if file_found.startswith(prefix + '.') and file_found.endswith('.' + values['extension']):
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96 if 'file' not in values:
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97 files_required[prefix]['file'] = file_path
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98 files_required[prefix]['modification'] = file_modification
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99 else:
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100 if file_modification > files_required[prefix]['modification']:
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101 files_required[prefix]['file'] = file_path
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102 files_required[prefix]['modification'] = file_modification
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103 return files_required
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104
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105
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106 def get_samples_run(sample_report_file):
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107 samples_run = {}
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108 with open(sample_report_file, 'rtU') as reader:
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109 for line in reader:
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110 line = line.splitlines()[0]
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111 if len(line) > 0:
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112 if not line.startswith('#'):
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113 sample_info = line.split('\t')
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114 if sample_info[1] not in samples_run:
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115 samples_run[sample_info[1]] = []
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116 samples_run[sample_info[1]].append(sample_info[0])
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117 return samples_run
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118
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119
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120 def get_rematch_command(log_file):
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121 variables = {'command': False, 'directory': False}
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122 with open(log_file, 'rtU') as reader:
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123 for line in reader:
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124 if any([isinstance(value, bool) for value in variables.values()]):
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125 line = line.splitlines()[0]
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126 if len(line) > 0:
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127 if line == 'COMMAND:':
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128 variables['command'] = True
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129 elif line == 'PRESENT DIRECTORY:':
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130 variables['directory'] = True
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131 else:
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132 if variables['command'] is True:
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133 variables['command'] = line.split(' ')
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134 elif variables['directory'] is True:
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135 variables['directory'] = line
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136 else:
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137 break
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138 command = {'command': [], 'listIDs': None, 'taxon': False, 'threads': None}
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139 if all([not isinstance(value, bool) for value in variables.values()]):
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140 counter = 0
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141 while counter < len(variables['command']):
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142 if variables['command'][counter].startswith('-'):
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143 if variables['command'][counter] not in ('-t', '--taxon'):
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144 if variables['command'][counter] in ('-l', '--listIDs'):
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145 command['listIDs'] = variables['command'][counter + 1]
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146 counter += 1
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147 elif variables['command'][counter] in ('-w', '--workdir'):
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148 counter += 1
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149 elif variables['command'][counter] in ('-j', '--threads'):
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150 command['threads'] = int(variables['command'][counter + 1])
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151 counter += 1
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152 elif variables['command'][counter] == '--mlst':
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153 species = []
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154 counter += 1
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155 while counter < len(variables['command']) and not variables['command'][counter].startswith('-'):
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156 if len(variables['command'][counter]) > 0:
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157 species.append(variables['command'][counter])
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158 counter += 1
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159 command['command'].extend(['--mlst', ' '.join(species)])
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160 else:
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161 command['command'].append(variables['command'][counter])
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162 if counter + 1 < len(variables['command']) and not variables['command'][counter + 1].startswith('-'):
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163 command['command'].append(variables['command'][counter + 1])
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164 counter += 1
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165 else:
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166 command['taxon'] = True
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167 for i in range(counter, len(variables['command'])):
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168 if i + 1 < len(variables['command']):
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169 if variables['command'][i + 1].startswith('-'):
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170 counter = i
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171 break
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172 else:
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173 counter = i
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174 else:
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175 command['command'].append(variables['command'][counter])
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176 counter += 1
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177 return command['command'], command['listIDs'], command['taxon'], command['threads'], variables['directory']
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178
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179
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180 def getTaxonRunIDs(IDs_list_seqFromWebTaxon_file):
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181 list_ids = []
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182 with open(IDs_list_seqFromWebTaxon_file, 'rtU') as reader:
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183 for line in reader:
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184 line = line.splitlines()[0]
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185 if len(line) > 0:
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186 if not line.startswith('#'):
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187 line = line.split('\t')
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188 list_ids.append(line[0])
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189 return list_ids
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190
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191
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192 def getListIDs_fromFile(listIDs_file):
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193 list_ids = []
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194 with open(listIDs_file, 'rtU') as lines:
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195 for line in lines:
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196 line = line.splitlines()[0]
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197 if len(line) > 0:
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198 list_ids.append(line)
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199 return list_ids
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200
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201
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202 def searchFastqFiles(initialWorkdir):
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203 filesExtensions = ['.fastq.gz', '.fq.gz']
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204 pairEnd_filesSeparation = [['_R1_001.f', '_R2_001.f'], ['_1.f', '_2.f']]
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205
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206 list_ids = {}
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207 directories = [d for d in os.listdir(initialWorkdir) if not d.startswith('.') and os.path.isdir(os.path.join(initialWorkdir, d, ''))]
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208 for directory_found in directories:
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209 directory_path = os.path.join(initialWorkdir, directory_found, '')
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210
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211 fastqFound = []
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212 files = [f for f in os.listdir(directory_path) if not f.startswith('.') and os.path.isfile(os.path.join(directory_path, f))]
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213 for file_found in files:
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214 if file_found.endswith(tuple(filesExtensions)):
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215 fastqFound.append(file_found)
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216
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217 if len(fastqFound) == 1:
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218 list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastqFound]
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219 elif len(fastqFound) >= 2:
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220 file_pair = []
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221
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222 # Search pairs
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223 for PE_separation in pairEnd_filesSeparation:
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224 for fastq in fastqFound:
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225 if PE_separation[0] in fastq or PE_separation[1] in fastq:
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226 file_pair.append(fastq)
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227
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228 if len(file_pair) == 2:
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229 break
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230 else:
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231 file_pair = []
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232
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233 # Search single
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234 if len(file_pair) == 0:
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235 for PE_separation in pairEnd_filesSeparation:
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236 for fastq in fastqFound:
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237 if PE_separation[0] not in fastq or PE_separation[1] not in fastq:
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238 file_pair.append(fastq)
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239
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240 if len(file_pair) >= 1:
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241 file_pair = file_pair[0]
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242
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243 if len(file_pair) >= 1:
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244 list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
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245
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246 return list_ids
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247
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248
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249 def setSamples_fromFolders(samples_to_run, samples_fastq, workdir):
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250 for sample in samples_to_run:
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251 sample_dir = os.path.join(workdir, sample, '')
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252 if not os.path.isdir(sample_dir):
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253 os.mkdir(sample_dir)
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254 for file_found in samples_fastq[sample]:
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255 link_path = os.path.join(sample_dir, os.path.basename(file_found))
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256 if os.path.islink(link_path):
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257 os.remove(link_path)
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258 if not os.path.isfile(link_path):
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259 os.symlink(file_found, link_path)
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260
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261
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262 def main():
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263 parser = argparse.ArgumentParser(prog='restart_rematch.py', description='Restart a ReMatCh run abruptly terminated', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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264 parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
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265
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266 parser_required = parser.add_argument_group('Required options')
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267 parser_required.add_argument('-i', '--initialWorkdir', type=str, metavar='/path/to/initial/workdir/directory/', help='Path to the directory where ReMatCh was running', required=True)
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268
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269 parser_optional_general = parser.add_argument_group('General facultative options')
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270 parser_optional_general.add_argument('-w', '--workdir', type=str, metavar='/path/to/workdir/directory/', help='Path to the directory where ReMatCh will run again', required=False, default='.')
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271 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use instead of the ones set in initial ReMatCh run', required=False)
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272 parser_optional_general.add_argument('--runFailedSamples', action='store_true', help='Will run ReMatCh for those samples missing, as well as for samples that did not run successfully in initial ReMatCh run')
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273
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274 args = parser.parse_args()
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275
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276 runRematch(args)
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277
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278
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279 if __name__ == "__main__":
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280 main()