--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/restart_rematch.py	Wed Jan 22 08:41:44 2020 -0500
@@ -0,0 +1,280 @@
+#!/usr/bin/env python
+
+# -*- coding: utf-8 -*-
+
+"""
+restart_rematch.py - Restarts a ReMatCh run abruptly terminated
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2017 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: February 09, 2017
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import os
+import argparse
+import subprocess
+import time
+
+
+version = '0.1'
+
+
+def runRematch(args):
+	print '\n' + '==========> Restarting ReMatCh <==========' + '\n'
+
+	workdir = os.path.abspath(args.workdir)
+	if not os.path.isdir(workdir):
+		os.makedirs(workdir)
+
+	initialWorkdir = os.path.abspath(args.initialWorkdir)
+
+	files_required = get_files_required(initialWorkdir)
+
+	samples_run = get_samples_run(files_required['sample_report']['file'])
+
+	command, list_ids, taxon, threads, initial_present_directory = get_rematch_command(files_required['run']['file'])
+
+	if list_ids is not None:
+		total_samples = getListIDs_fromFile(list_ids)
+	elif taxon:
+		total_samples = getTaxonRunIDs(files_required['IDs_list.seqFromWebTaxon']['file'])
+	else:
+		samples_fastq = searchFastqFiles(initialWorkdir)
+		total_samples = samples_fastq.keys()
+
+	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 [''])))
+
+	print str(len(samples_to_run)) + ' samples out of ' + str(len(total_samples)) + ' will be analysed by ReMatCh' + '\n'
+
+	if list_ids is not None or taxon:
+		samples_to_run_file = write_samples_to_run(samples_to_run, workdir)
+	else:
+		setSamples_fromFolders(samples_to_run, samples_fastq, workdir)
+
+	command.extend(['-w', workdir])
+	command.extend(['-j', str(threads) if args.threads is None else str(args.threads)])
+	if list_ids is not None or taxon:
+		command.extend(['-l', samples_to_run_file])
+
+	print 'ReMatCh will start in 5 seconds...'
+	time.sleep(5)
+
+	os.chdir(initial_present_directory)
+	subprocess.call(command)
+
+
+def write_samples_to_run(samples_to_run, workdir):
+	samples_to_run_file = os.path.join(workdir, 'restart_rematch.samples_to_run.txt')
+	with open(samples_to_run_file, 'wt') as writer:
+		for sample in samples_to_run:
+			writer.write(sample + '\n')
+	return samples_to_run_file
+
+
+def get_files_required(initialWorkdir):
+	files_required = {'sample_report': {'extension': 'tab'}, 'run': {'extension': 'log'}, 'IDs_list.seqFromWebTaxon': {'extension': 'tab'}}
+	files = sorted([f for f in os.listdir(initialWorkdir) if not f.startswith('.') and os.path.isfile(os.path.join(initialWorkdir, f))])
+	for file_found in files:
+		file_path = os.path.join(initialWorkdir, file_found)
+		file_modification = os.path.getmtime(file_path)
+		for prefix, values in files_required.items():
+			if file_found.startswith(prefix + '.') and file_found.endswith('.' + values['extension']):
+				if 'file' not in values:
+					files_required[prefix]['file'] = file_path
+					files_required[prefix]['modification'] = file_modification
+				else:
+					if file_modification > files_required[prefix]['modification']:
+						files_required[prefix]['file'] = file_path
+						files_required[prefix]['modification'] = file_modification
+	return files_required
+
+
+def get_samples_run(sample_report_file):
+	samples_run = {}
+	with open(sample_report_file, 'rtU') as reader:
+		for line in reader:
+			line = line.splitlines()[0]
+			if len(line) > 0:
+				if not line.startswith('#'):
+					sample_info = line.split('\t')
+					if sample_info[1] not in samples_run:
+						samples_run[sample_info[1]] = []
+					samples_run[sample_info[1]].append(sample_info[0])
+	return samples_run
+
+
+def get_rematch_command(log_file):
+	variables = {'command': False, 'directory': False}
+	with open(log_file, 'rtU') as reader:
+		for line in reader:
+			if any([isinstance(value, bool) for value in variables.values()]):
+				line = line.splitlines()[0]
+				if len(line) > 0:
+					if line == 'COMMAND:':
+						variables['command'] = True
+					elif line == 'PRESENT DIRECTORY:':
+						variables['directory'] = True
+					else:
+						if variables['command'] is True:
+							variables['command'] = line.split(' ')
+						elif variables['directory'] is True:
+							variables['directory'] = line
+			else:
+				break
+	command = {'command': [], 'listIDs': None, 'taxon': False, 'threads': None}
+	if all([not isinstance(value, bool) for value in variables.values()]):
+		counter = 0
+		while counter < len(variables['command']):
+			if variables['command'][counter].startswith('-'):
+				if variables['command'][counter] not in ('-t', '--taxon'):
+					if variables['command'][counter] in ('-l', '--listIDs'):
+						command['listIDs'] = variables['command'][counter + 1]
+						counter += 1
+					elif variables['command'][counter] in ('-w', '--workdir'):
+						counter += 1
+					elif variables['command'][counter] in ('-j', '--threads'):
+						command['threads'] = int(variables['command'][counter + 1])
+						counter += 1
+					elif variables['command'][counter] == '--mlst':
+						species = []
+						counter += 1
+						while counter < len(variables['command']) and not variables['command'][counter].startswith('-'):
+							if len(variables['command'][counter]) > 0:
+								species.append(variables['command'][counter])
+							counter += 1
+						command['command'].extend(['--mlst', ' '.join(species)])
+					else:
+						command['command'].append(variables['command'][counter])
+						if counter + 1 < len(variables['command']) and not variables['command'][counter + 1].startswith('-'):
+							command['command'].append(variables['command'][counter + 1])
+							counter += 1
+				else:
+					command['taxon'] = True
+					for i in range(counter, len(variables['command'])):
+						if i + 1 < len(variables['command']):
+							if variables['command'][i + 1].startswith('-'):
+								counter = i
+								break
+						else:
+							counter = i
+			else:
+				command['command'].append(variables['command'][counter])
+			counter += 1
+	return command['command'], command['listIDs'], command['taxon'], command['threads'], variables['directory']
+
+
+def getTaxonRunIDs(IDs_list_seqFromWebTaxon_file):
+	list_ids = []
+	with open(IDs_list_seqFromWebTaxon_file, 'rtU') as reader:
+		for line in reader:
+			line = line.splitlines()[0]
+			if len(line) > 0:
+				if not line.startswith('#'):
+					line = line.split('\t')
+					list_ids.append(line[0])
+	return list_ids
+
+
+def getListIDs_fromFile(listIDs_file):
+	list_ids = []
+	with open(listIDs_file, 'rtU') as lines:
+		for line in lines:
+			line = line.splitlines()[0]
+			if len(line) > 0:
+				list_ids.append(line)
+	return list_ids
+
+
+def searchFastqFiles(initialWorkdir):
+	filesExtensions = ['.fastq.gz', '.fq.gz']
+	pairEnd_filesSeparation = [['_R1_001.f', '_R2_001.f'], ['_1.f', '_2.f']]
+
+	list_ids = {}
+	directories = [d for d in os.listdir(initialWorkdir) if not d.startswith('.') and os.path.isdir(os.path.join(initialWorkdir, d, ''))]
+	for directory_found in directories:
+		directory_path = os.path.join(initialWorkdir, directory_found, '')
+
+		fastqFound = []
+		files = [f for f in os.listdir(directory_path) if not f.startswith('.') and os.path.isfile(os.path.join(directory_path, f))]
+		for file_found in files:
+			if file_found.endswith(tuple(filesExtensions)):
+				fastqFound.append(file_found)
+
+		if len(fastqFound) == 1:
+			list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastqFound]
+		elif len(fastqFound) >= 2:
+			file_pair = []
+
+			# Search pairs
+			for PE_separation in pairEnd_filesSeparation:
+				for fastq in fastqFound:
+					if PE_separation[0] in fastq or PE_separation[1] in fastq:
+						file_pair.append(fastq)
+
+				if len(file_pair) == 2:
+					break
+				else:
+					file_pair = []
+
+			# Search single
+			if len(file_pair) == 0:
+				for PE_separation in pairEnd_filesSeparation:
+					for fastq in fastqFound:
+						if PE_separation[0] not in fastq or PE_separation[1] not in fastq:
+							file_pair.append(fastq)
+
+				if len(file_pair) >= 1:
+					file_pair = file_pair[0]
+
+			if len(file_pair) >= 1:
+				list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
+
+	return list_ids
+
+
+def setSamples_fromFolders(samples_to_run, samples_fastq, workdir):
+	for sample in samples_to_run:
+		sample_dir = os.path.join(workdir, sample, '')
+		if not os.path.isdir(sample_dir):
+			os.mkdir(sample_dir)
+		for file_found in samples_fastq[sample]:
+			link_path = os.path.join(sample_dir, os.path.basename(file_found))
+			if os.path.islink(link_path):
+				os.remove(link_path)
+			if not os.path.isfile(link_path):
+				os.symlink(file_found, link_path)
+
+
+def main():
+	parser = argparse.ArgumentParser(prog='restart_rematch.py', description='Restart a ReMatCh run abruptly terminated', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+	parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+	parser_required = parser.add_argument_group('Required options')
+	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)
+
+	parser_optional_general = parser.add_argument_group('General facultative options')
+	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='.')
+	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)
+	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')
+
+	args = parser.parse_args()
+
+	runRematch(args)
+
+
+if __name__ == "__main__":
+	main()