Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/ReMatCh/utils/restart_rematch.py @ 3:0cbed1c0a762 draft default tip

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author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
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1 #!/usr/bin/env python3
0
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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) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
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10
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11 Last modified: October 15, 2018
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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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33 version = '0.1'
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35
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36 def run_rematch(args):
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37 print('\n' + '==========> Restarting ReMatCh <==========' + '\n')
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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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43 initial_workdir = os.path.abspath(args.initialWorkdir)
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45 files_required = get_files_required(initial_workdir)
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47 samples_run = get_samples_run(files_required['sample_report']['file'])
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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 samples_fastq = {}
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52
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53 if list_ids is not None:
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54 total_samples = get_list_ids_from_file(list_ids)
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55 elif taxon:
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56 total_samples = get_taxon_run_ids(files_required['IDs_list.seqFromWebTaxon']['file'])
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57 else:
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58 samples_fastq = search_fastq_files(initial_workdir)
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59 total_samples = list(samples_fastq.keys())
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61 samples_to_run = list(set(total_samples).symmetric_difference(set(sum(list(samples_run.values()), []) if
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62 not args.runFailedSamples else
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63 samples_run['True'] if
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64 'True' in samples_run else [''])))
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65
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66 print(str(len(samples_to_run)) + ' samples out of ' + str(len(total_samples)) + ' will be analysed by'
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67 ' ReMatCh' + '\n')
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68
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69 if list_ids is not None or taxon:
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70 samples_to_run_file = write_samples_to_run(samples_to_run, workdir)
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71 else:
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72 set_samples_from_folders(samples_to_run, samples_fastq, workdir)
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73
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74 command.extend(['-w', workdir])
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75 command.extend(['-j', str(threads) if args.threads is None else str(args.threads)])
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76 if list_ids is not None or taxon:
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77 command.extend(['-l', samples_to_run_file])
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78
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79 print('ReMatCh will start in 5 seconds...')
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80 time.sleep(5)
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81
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82 os.chdir(initial_present_directory)
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83 subprocess.call(command)
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84
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85
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86 def write_samples_to_run(samples_to_run, workdir):
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87 samples_to_run_file = os.path.join(workdir, 'restart_rematch.samples_to_run.txt')
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88 with open(samples_to_run_file, 'wt') as writer:
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89 for sample in samples_to_run:
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90 writer.write(sample + '\n')
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91 return samples_to_run_file
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92
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93
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94 def get_files_required(initial_workdir):
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95 files_required = {'sample_report': {'extension': 'tab'},
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96 'run': {'extension': 'log'},
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97 'IDs_list.seqFromWebTaxon': {'extension': 'tab'}}
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98 files = sorted([f for f in os.listdir(initial_workdir) if
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99 not f.startswith('.') and
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100 os.path.isfile(os.path.join(initial_workdir, f))])
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101 for file_found in files:
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102 file_path = os.path.join(initial_workdir, file_found)
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103 file_modification = os.path.getmtime(file_path)
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104 for prefix, values in list(files_required.items()):
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105 if file_found.startswith(prefix + '.') and file_found.endswith('.' + values['extension']):
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106 if 'file' not in values:
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107 files_required[prefix]['file'] = file_path
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108 files_required[prefix]['modification'] = file_modification
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109 else:
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110 if file_modification > files_required[prefix]['modification']:
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111 files_required[prefix]['file'] = file_path
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112 files_required[prefix]['modification'] = file_modification
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113 return files_required
0
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114
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115
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116 def get_samples_run(sample_report_file):
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117 samples_run = {}
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118 with open(sample_report_file, 'rtU') as reader:
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119 for line in reader:
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120 line = line.splitlines()[0]
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121 if len(line) > 0:
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122 if not line.startswith('#'):
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123 sample_info = line.split('\t')
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124 if sample_info[1] not in samples_run:
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125 samples_run[sample_info[1]] = []
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126 samples_run[sample_info[1]].append(sample_info[0])
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127 return samples_run
0
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128
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129
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130 def get_rematch_command(log_file):
3
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131 variables = {'command': False, 'directory': False}
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132 with open(log_file, 'rtU') as reader:
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133 for line in reader:
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134 if any([isinstance(value, bool) for value in list(variables.values())]):
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135 line = line.splitlines()[0]
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136 if len(line) > 0:
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137 if line == 'COMMAND:':
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138 variables['command'] = True
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139 elif line == 'PRESENT DIRECTORY:':
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140 variables['directory'] = True
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141 else:
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142 if variables['command'] is True:
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143 variables['command'] = line.split(' ')
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144 elif variables['directory'] is True:
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145 variables['directory'] = line
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146 else:
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147 break
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148 command = {'command': [], 'listIDs': None, 'taxon': False, 'threads': None}
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149 if all([not isinstance(value, bool) for value in list(variables.values())]):
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150 counter = 0
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151 while counter < len(variables['command']):
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152 if variables['command'][counter].startswith('-'):
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153 if variables['command'][counter] not in ('-t', '--taxon'):
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154 if variables['command'][counter] in ('-l', '--listIDs'):
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155 command['listIDs'] = variables['command'][counter + 1]
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156 counter += 1
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157 elif variables['command'][counter] in ('-w', '--workdir'):
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158 counter += 1
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159 elif variables['command'][counter] in ('-j', '--threads'):
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160 command['threads'] = int(variables['command'][counter + 1])
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161 counter += 1
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162 elif variables['command'][counter] == '--mlst':
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163 species = []
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164 counter += 1
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165 while counter < len(variables['command']) and not variables['command'][counter].startswith('-'):
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166 if len(variables['command'][counter]) > 0:
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167 species.append(variables['command'][counter])
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168 counter += 1
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169 command['command'].extend(['--mlst', ' '.join(species)])
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170 else:
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171 command['command'].append(variables['command'][counter])
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172 if counter + 1 < len(variables['command']) and \
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173 not variables['command'][counter + 1].startswith('-'):
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174 command['command'].append(variables['command'][counter + 1])
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175 counter += 1
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176 else:
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177 command['taxon'] = True
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178 for i in range(counter, len(variables['command'])):
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179 if i + 1 < len(variables['command']):
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180 if variables['command'][i + 1].startswith('-'):
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181 counter = i
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182 break
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183 else:
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184 counter = i
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185 else:
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186 command['command'].append(variables['command'][counter])
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187 counter += 1
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188 return command['command'], command['listIDs'], command['taxon'], command['threads'], variables['directory']
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189
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190
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191 def get_taxon_run_ids(ids_list_seq_from_web_taxon_file):
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192 list_ids = []
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193 with open(ids_list_seq_from_web_taxon_file, 'rtU') as reader:
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194 for line in reader:
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195 line = line.splitlines()[0]
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196 if len(line) > 0:
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197 if not line.startswith('#'):
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198 line = line.split('\t')
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199 list_ids.append(line[0])
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200 return list_ids
0
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201
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202
3
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203 def get_list_ids_from_file(list_ids_file):
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204 list_ids = []
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205 with open(list_ids_file, 'rtU') as lines:
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206 for line in lines:
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207 line = line.splitlines()[0]
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208 if len(line) > 0:
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209 list_ids.append(line)
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210 return list_ids
0
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211
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212
3
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213 def search_fastq_files(initial_workdir):
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214 files_extensions = ['.fastq.gz', '.fq.gz']
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215 pair_end_files_separation = [['_R1_001.f', '_R2_001.f'], ['_1.f', '_2.f']]
0
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216
3
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217 list_ids = {}
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218 directories = [d for d in os.listdir(initial_workdir) if
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219 not d.startswith('.') and
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220 os.path.isdir(os.path.join(initial_workdir, d, ''))]
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221 for directory_found in directories:
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222 directory_path = os.path.join(initial_workdir, directory_found, '')
0
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223
3
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224 fastq_found = []
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225 files = [f for f in os.listdir(directory_path) if
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226 not f.startswith('.') and
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227 os.path.isfile(os.path.join(directory_path, f))]
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228 for file_found in files:
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229 if file_found.endswith(tuple(files_extensions)):
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230 fastq_found.append(file_found)
0
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231
3
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232 if len(fastq_found) == 1:
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233 list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastq_found]
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234 elif len(fastq_found) >= 2:
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235 file_pair = []
0
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236
3
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237 # Search pairs
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238 for pe_separation in pair_end_files_separation:
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239 for fastq in fastq_found:
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240 if pe_separation[0] in fastq or pe_separation[1] in fastq:
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241 file_pair.append(fastq)
0
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242
3
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243 if len(file_pair) == 2:
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244 break
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245 else:
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246 file_pair = []
0
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247
3
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248 # Search single
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249 if len(file_pair) == 0:
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250 for pe_separation in pair_end_files_separation:
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251 for fastq in fastq_found:
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252 if pe_separation[0] not in fastq or pe_separation[1] not in fastq:
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253 file_pair.append(fastq)
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254
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255 if len(file_pair) >= 1:
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256 file_pair = file_pair[0]
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257
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258 if len(file_pair) >= 1:
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259 list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
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260
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261 return list_ids
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262
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263
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264 def set_samples_from_folders(samples_to_run, samples_fastq, workdir):
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265 for sample in samples_to_run:
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266 sample_dir = os.path.join(workdir, sample, '')
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267 if not os.path.isdir(sample_dir):
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268 os.mkdir(sample_dir)
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269 for file_found in samples_fastq[sample]:
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270 link_path = os.path.join(sample_dir, os.path.basename(file_found))
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271 if os.path.islink(link_path):
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272 os.remove(link_path)
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273 if not os.path.isfile(link_path):
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274 os.symlink(file_found, link_path)
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275
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276
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277 def main():
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278 parser = argparse.ArgumentParser(prog='restart_rematch.py', description='Restart a ReMatCh run abruptly terminated',
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279 formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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280 parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
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281
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282 parser_required = parser.add_argument_group('Required options')
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283 parser_required.add_argument('-i', '--initialWorkdir', type=str, metavar='/path/to/initial/workdir/directory/',
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284 help='Path to the directory where ReMatCh was running', required=True)
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285
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286 parser_optional_general = parser.add_argument_group('General facultative options')
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287 parser_optional_general.add_argument('-w', '--workdir', type=str, metavar='/path/to/workdir/directory/',
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288 help='Path to the directory where ReMatCh will run again', required=False,
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289 default='.')
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290 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N',
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291 help='Number of threads to use instead of the ones set in initial ReMatCh run',
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292 required=False)
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293 parser_optional_general.add_argument('--runFailedSamples', action='store_true',
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294 help='Will run ReMatCh for those samples missing, as well as for samples that'
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295 ' did not run successfully in initial ReMatCh run')
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296
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297 args = parser.parse_args()
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298
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299 run_rematch(args)
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300
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301
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302 if __name__ == "__main__":
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303 main()