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1 #!/usr/bin/env python3
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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 rematch.py - Reads mapping against target sequences, checking mapping
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7 and consensus sequences production
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8 <https://github.com/B-UMMI/ReMatCh/>
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9
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10 Copyright (C) 2019 Miguel Machado <mpmachado@medicina.ulisboa.pt>
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11
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12 Last modified: August 08, 2019
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13
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14 This program is free software: you can redistribute it and/or modify
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15 it under the terms of the GNU General Public License as published by
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16 the Free Software Foundation, either version 3 of the License, or
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17 (at your option) any later version.
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18
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19 This program is distributed in the hope that it will be useful,
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20 but WITHOUT ANY WARRANTY; without even the implied warranty of
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21 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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22 GNU General Public License for more details.
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23
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24 You should have received a copy of the GNU General Public License
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25 along with this program. If not, see <http://www.gnu.org/licenses/>.
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26 """
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27
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28 import os
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29 import sys
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30 import time
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31 import argparse
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32
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33 try:
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34 from __init__ import __version__
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35
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36 import modules.utils as utils
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37 import modules.seqFromWebTaxon as seq_from_web_taxon
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38 import modules.download as download
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39 import modules.rematch_module as rematch_module
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40 import modules.checkMLST as check_mlst
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41 except ImportError:
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42 from ReMatCh.__init__ import __version__
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43
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44 from ReMatCh.modules import utils as utils
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45 from ReMatCh.modules import seqFromWebTaxon as seq_from_web_taxon
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46 from ReMatCh.modules import download as download
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47 from ReMatCh.modules import rematch_module as rematch_module
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48 from ReMatCh.modules import checkMLST as check_mlst
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49
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50
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51 def search_fastq_files(directory):
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52 files_extensions = ['.fastq.gz', '.fq.gz']
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53 pair_end_files_separation = [['_R1_001.f', '_R2_001.f'], ['_1.f', '_2.f']]
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54
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55 list_ids = {}
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56 directories = [d for d in os.listdir(directory) if
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57 not d.startswith('.') and os.path.isdir(os.path.join(directory, d, ''))]
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58 for directory_found in directories:
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59 if directory_found != 'pubmlst':
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60 directory_path = os.path.join(directory, directory_found, '')
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61
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62 fastq_found = []
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63 files = [f for f in os.listdir(directory_path) if
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64 not f.startswith('.') and os.path.isfile(os.path.join(directory_path, f))]
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65 for file_found in files:
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66 if file_found.endswith(tuple(files_extensions)):
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67 fastq_found.append(file_found)
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68
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69 if len(fastq_found) == 1:
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70 list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastq_found]
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71 elif len(fastq_found) >= 2:
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72 file_pair = []
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73
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74 # Search pairs
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75 for pe_separation in pair_end_files_separation:
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76 for fastq in fastq_found:
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77 if pe_separation[0] in fastq or pe_separation[1] in fastq:
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78 file_pair.append(fastq)
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79
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80 if len(file_pair) == 2:
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81 break
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82 else:
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83 file_pair = []
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84
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85 # Search single
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86 if len(file_pair) == 0:
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87 for pe_separation in pair_end_files_separation:
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88 for fastq in fastq_found:
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89 if pe_separation[0] not in fastq or pe_separation[1] not in fastq:
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90 file_pair.append(fastq)
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91
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92 if len(file_pair) >= 1:
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93 file_pair = file_pair[0]
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94
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95 if len(file_pair) >= 1:
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96 list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
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97
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98 return list_ids
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99
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100
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101 def get_list_ids_from_file(file_list_ids):
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102 list_ids = []
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103
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104 with open(file_list_ids, 'rtU') as lines:
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105 for line in lines:
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106 line = line.rstrip('\r\n')
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107 if len(line) > 0:
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108 list_ids.append(line)
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109
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110 if len(list_ids) == 0:
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111 sys.exit('No runIDs were found in ' + file_list_ids)
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112
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113 return list_ids
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114
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115
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116 def get_taxon_run_ids(taxon_name, outputfile):
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117 seq_from_web_taxon.run_seq_from_web_taxon(taxon_name, outputfile, True, True, True, False)
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118
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119 run_ids = []
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120 with open(outputfile, 'rtU') as reader:
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121 for line in reader:
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122 line = line.rstrip('\r\n')
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123 if len(line) > 0:
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124 if not line.startswith('#'):
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125 line = line.split('\t')
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126 run_ids.append(line[0])
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127
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128 return run_ids
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129
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130
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131 def get_list_ids(workdir, file_list_ids, taxon_name):
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132 searched_fastq_files = False
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133 list_ids = []
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134 if file_list_ids is None and taxon_name is None:
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135 list_ids = search_fastq_files(workdir)
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136 searched_fastq_files = True
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137 elif file_list_ids is not None:
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138 list_ids = get_list_ids_from_file(os.path.abspath(file_list_ids))
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139 elif taxon_name is not None and file_list_ids is None:
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140 list_ids = get_taxon_run_ids(taxon_name, os.path.join(workdir, 'IDs_list.seqFromWebTaxon.tab'))
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141
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142 if len(list_ids) == 0:
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143 sys.exit('No IDs were found')
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144 return list_ids, searched_fastq_files
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145
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146
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147 def format_gene_info(gene_specific_info, minimum_gene_coverage, minimum_gene_identity, reported_data_type, summary,
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148 sample, genes_present):
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149 info = None
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150 if gene_specific_info['gene_coverage'] >= minimum_gene_coverage and \
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151 gene_specific_info['gene_identity'] >= minimum_gene_identity:
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152 if summary and sample not in genes_present:
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153 genes_present[sample] = {}
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154
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155 if gene_specific_info['gene_number_positions_multiple_alleles'] == 0:
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156 s = str(gene_specific_info[reported_data_type])
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157 info = str(s)
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158 if summary:
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159 genes_present[sample][gene_specific_info['header']] = str(s)
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160 else:
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161 s = 'multiAlleles_' + str(gene_specific_info[reported_data_type])
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162 info = str(s)
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163 if summary:
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164 genes_present[sample][gene_specific_info['header']] = str(s)
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165 else:
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166 info = 'absent_' + str(gene_specific_info[reported_data_type])
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167
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168 return info, genes_present
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169
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170
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171 def write_data_by_gene(gene_list_reference, minimum_gene_coverage, sample, data_by_gene, outdir, time_str, run_times,
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172 minimum_gene_identity, reported_data_type, summary, genes_present):
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173 combined_report = \
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174 os.path.join(outdir,
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175 'combined_report.data_by_gene.' + run_times + '.' + reported_data_type + '.' + time_str + '.tab')
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176
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177 if reported_data_type == 'coverage_depth':
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178 reported_data_type = 'gene_mean_read_coverage'
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179 elif reported_data_type == 'sequence_coverage':
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180 reported_data_type = 'gene_coverage'
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181
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182 combined_report_exist = os.path.isfile(combined_report)
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183 with open(combined_report, 'at') as writer:
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184 seq_list = sorted(gene_list_reference.keys())
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185 if not combined_report_exist:
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186 writer.write('#sample' + '\t' + '\t'.join([gene_list_reference[seq] for seq in seq_list]) + '\n')
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187
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188 results = {}
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189 headers = []
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190 for i in data_by_gene:
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191 results[data_by_gene[i]['header']], genes_present = format_gene_info(data_by_gene[i], minimum_gene_coverage,
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192 minimum_gene_identity,
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193 reported_data_type, summary, sample,
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194 genes_present)
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195 headers.append(data_by_gene[i]['header'])
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196
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197 if len(headers) != gene_list_reference:
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198 for gene in gene_list_reference:
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199 if gene not in headers:
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200 results[gene] = 'NA'
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201
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202 writer.write(sample + '\t' + '\t'.join([results[seq] for seq in seq_list]) + '\n')
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203
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204 return genes_present
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205
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206
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207 def write_sample_report(sample, outdir, time_str, file_size, run_successfully_fastq, run_successfully_rematch_first,
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208 run_successfully_rematch_second, time_taken_fastq, time_taken_rematch_first,
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209 time_taken_rematch_second, time_taken_sample, sequencing_information, sample_data_general_first,
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210 sample_data_general_second, fastq_used):
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211 sample_report = os.path.join(outdir, 'sample_report.' + time_str + '.tab')
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212 report_exist = os.path.isfile(sample_report)
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213
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214 header_general = ['sample', 'sample_run_successfully', 'sample_run_time', 'files_size', 'download_run_successfully',
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215 'download_run_time', 'rematch_run_successfully_first', 'rematch_run_time_first',
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216 'rematch_run_successfully_second', 'rematch_run_time_second']
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217 header_data_general = ['number_absent_genes', 'number_genes_multiple_alleles', 'mean_sample_coverage']
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218 header_sequencing = ['run_accession', 'instrument_platform', 'instrument_model', 'library_layout', 'library_source',
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219 'extra_run_accession', 'nominal_length', 'read_count', 'base_count', 'date_download']
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220
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221 with open(sample_report, 'at') as writer:
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222 if not report_exist:
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223 writer.write('#' + '\t'.join(header_general) + '\t' + '_first\t'.join(header_data_general) + '_first\t' +
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224 '_second\t'.join(header_data_general) + '_second\t' + '\t'.join(header_sequencing) + '\t' +
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225 'fastq_used' + '\n')
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226
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227 writer.write('\t'.join([sample,
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228 str(all([run_successfully_fastq is not False,
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229 run_successfully_rematch_first is not False,
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230 run_successfully_rematch_second is not False])),
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231 str(time_taken_sample),
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232 str(file_size),
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233 str(run_successfully_fastq),
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234 str(time_taken_fastq),
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235 str(run_successfully_rematch_first),
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236 str(time_taken_rematch_first),
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237 str(run_successfully_rematch_second),
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238 str(time_taken_rematch_second)]) +
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239 '\t' + '\t'.join([str(sample_data_general_first[i]) for i in header_data_general]) +
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240 '\t' + '\t'.join([str(sample_data_general_second[i]) for i in header_data_general]) +
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241 '\t' + '\t'.join([str(sequencing_information[i]) for i in header_sequencing]) +
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242 '\t' + ','.join(fastq_used) + '\n')
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243
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244
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245 def concatenate_extra_seq_2_consensus(consensus_sequence, reference_sequence, extra_seq_length, outdir):
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246 reference_dict, ignore, ignore = rematch_module.get_sequence_information(reference_sequence, extra_seq_length)
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247 consensus_dict, genes, ignore = rematch_module.get_sequence_information(consensus_sequence, 0)
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248 number_consensus_with_sequences = 0
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249 for k, values_consensus in list(consensus_dict.items()):
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250 for values_reference in list(reference_dict.values()):
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251 if values_reference['header'] == values_consensus['header']:
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252 if len(set(consensus_dict[k]['sequence'])) > 1:
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253 number_consensus_with_sequences += 1
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254 if extra_seq_length <= len(values_reference['sequence']):
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255 right_extra_seq = \
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256 '' if extra_seq_length == 0 else values_reference['sequence'][-extra_seq_length:]
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257 consensus_dict[k]['sequence'] = \
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258 values_reference['sequence'][:extra_seq_length] + \
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259 consensus_dict[k]['sequence'] + \
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260 right_extra_seq
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261 consensus_dict[k]['length'] += extra_seq_length + len(right_extra_seq)
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262
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263 consensus_concatenated = os.path.join(outdir, 'consensus_concatenated_extraSeq.fasta')
|
|
cstrittmatter@0
|
264 with open(consensus_concatenated, 'wt') as writer:
|
|
cstrittmatter@0
|
265 for i in consensus_dict:
|
|
cstrittmatter@0
|
266 writer.write('>' + consensus_dict[i]['header'] + '\n')
|
|
cstrittmatter@0
|
267 fasta_sequence_lines = rematch_module.chunkstring(consensus_dict[i]['sequence'], 80)
|
|
cstrittmatter@0
|
268 for line in fasta_sequence_lines:
|
|
cstrittmatter@0
|
269 writer.write(line + '\n')
|
|
cstrittmatter@0
|
270
|
|
cstrittmatter@0
|
271 return consensus_concatenated, genes, consensus_dict, number_consensus_with_sequences
|
|
cstrittmatter@0
|
272
|
|
cstrittmatter@0
|
273
|
|
cstrittmatter@0
|
274 def clean_headers_reference_file(reference_file, outdir, extra_seq):
|
|
cstrittmatter@0
|
275 problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
|
|
cstrittmatter@0
|
276 print('Checking if reference sequences contain ' + str(problematic_characters) + '\n')
|
|
cstrittmatter@0
|
277 # headers_changed = False
|
|
cstrittmatter@0
|
278 new_reference_file = str(reference_file)
|
|
cstrittmatter@0
|
279 sequences, genes, headers_changed = rematch_module.get_sequence_information(reference_file, extra_seq)
|
|
cstrittmatter@0
|
280 if headers_changed:
|
|
cstrittmatter@0
|
281 print('At least one of the those characters was found. Replacing those with _' + '\n')
|
|
cstrittmatter@0
|
282 new_reference_file = \
|
|
cstrittmatter@0
|
283 os.path.join(outdir, os.path.splitext(os.path.basename(reference_file))[0] + '.headers_renamed.fasta')
|
|
cstrittmatter@0
|
284 with open(new_reference_file, 'wt') as writer:
|
|
cstrittmatter@0
|
285 for i in sequences:
|
|
cstrittmatter@0
|
286 writer.write('>' + sequences[i]['header'] + '\n')
|
|
cstrittmatter@0
|
287 fasta_sequence_lines = rematch_module.chunkstring(sequences[i]['sequence'], 80)
|
|
cstrittmatter@0
|
288 for line in fasta_sequence_lines:
|
|
cstrittmatter@0
|
289 writer.write(line + '\n')
|
|
cstrittmatter@0
|
290 return new_reference_file, genes, sequences
|
|
cstrittmatter@0
|
291
|
|
cstrittmatter@0
|
292
|
|
cstrittmatter@0
|
293 def write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, loci_order, outdir, time_str):
|
|
cstrittmatter@0
|
294 mlst_report = os.path.join(outdir, 'mlst_report.' + time_str + '.tab')
|
|
cstrittmatter@0
|
295 mlst_report_exist = os.path.isfile(mlst_report)
|
|
cstrittmatter@0
|
296 with open(mlst_report, 'at') as writer:
|
|
cstrittmatter@0
|
297 if not mlst_report_exist:
|
|
cstrittmatter@0
|
298 writer.write('\t'.join(['#sample', 'ReMatCh_run', 'consensus_type', 'ST'] + loci_order) + '\n')
|
|
cstrittmatter@0
|
299 writer.write('\t'.join([sample, run_times, consensus_type, str(st)] + alleles_profile.split(',')) + '\n')
|
|
cstrittmatter@0
|
300
|
|
cstrittmatter@0
|
301
|
|
cstrittmatter@0
|
302 def run_get_st(sample, mlst_dicts, consensus_sequences, mlst_consensus, run_times, outdir, time_str):
|
|
cstrittmatter@0
|
303 if mlst_consensus == 'all':
|
|
cstrittmatter@0
|
304 for consensus_type in consensus_sequences:
|
|
cstrittmatter@0
|
305 print('Searching MLST for ' + consensus_type + ' consensus')
|
|
cstrittmatter@0
|
306 st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[consensus_type])
|
|
cstrittmatter@0
|
307 write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, mlst_dicts[2], outdir, time_str)
|
|
cstrittmatter@0
|
308 print('ST found: ' + str(st) + ' (' + alleles_profile + ')')
|
|
cstrittmatter@0
|
309 else:
|
|
cstrittmatter@0
|
310 st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[mlst_consensus])
|
|
cstrittmatter@0
|
311 write_mlst_report(sample, run_times, mlst_consensus, st, alleles_profile, mlst_dicts[2], outdir, time_str)
|
|
cstrittmatter@0
|
312 print('ST found for ' + mlst_consensus + ' consensus: ' + str(st) + ' (' + alleles_profile + ')')
|
|
cstrittmatter@0
|
313
|
|
cstrittmatter@0
|
314
|
|
cstrittmatter@0
|
315 def write_summary_report(outdir, reported_data_type, time_str, gene_list_reference, genes_present):
|
|
cstrittmatter@0
|
316 with open(os.path.join(outdir,
|
|
cstrittmatter@0
|
317 'summary.{reported_data_type}.{time_str}.tab'.format(reported_data_type=reported_data_type,
|
|
cstrittmatter@0
|
318 time_str=time_str)), 'wt') as writer:
|
|
cstrittmatter@0
|
319 seq_list = []
|
|
cstrittmatter@0
|
320 for info in list(genes_present.values()):
|
|
cstrittmatter@0
|
321 seq_list.extend(list(info.keys()))
|
|
cstrittmatter@0
|
322 seq_list = list(set(seq_list))
|
|
cstrittmatter@0
|
323 writer.write('#sample' + '\t' + '\t'.join([gene_list_reference[seq] for seq in sorted(seq_list)]) + '\n')
|
|
cstrittmatter@0
|
324 for sample, info in list(genes_present.items()):
|
|
cstrittmatter@0
|
325 data = []
|
|
cstrittmatter@0
|
326 for seq in sorted(seq_list):
|
|
cstrittmatter@0
|
327 if seq in info:
|
|
cstrittmatter@0
|
328 data.append(info[seq])
|
|
cstrittmatter@0
|
329 else:
|
|
cstrittmatter@0
|
330 data.append('NF')
|
|
cstrittmatter@0
|
331 writer.write(sample + '\t' + '\t'.join(data) + '\n')
|
|
cstrittmatter@0
|
332
|
|
cstrittmatter@0
|
333
|
|
cstrittmatter@0
|
334 def run_rematch(args):
|
|
cstrittmatter@0
|
335 workdir = os.path.abspath(args.workdir)
|
|
cstrittmatter@0
|
336 if not os.path.isdir(workdir):
|
|
cstrittmatter@0
|
337 os.makedirs(workdir)
|
|
cstrittmatter@0
|
338
|
|
cstrittmatter@0
|
339 aspera_key = os.path.abspath(args.asperaKey.name) if args.asperaKey is not None else None
|
|
cstrittmatter@0
|
340
|
|
cstrittmatter@0
|
341 # Start logger
|
|
cstrittmatter@0
|
342 logfile, time_str = utils.start_logger(workdir)
|
|
cstrittmatter@0
|
343
|
|
cstrittmatter@0
|
344 # Get general information
|
|
cstrittmatter@0
|
345 script_path = utils.general_information(logfile, __version__, workdir, time_str, args.doNotUseProvidedSoftware,
|
|
cstrittmatter@0
|
346 aspera_key, args.downloadCramBam, args.SRA, args.SRAopt)
|
|
cstrittmatter@0
|
347
|
|
cstrittmatter@0
|
348 # Set list_ids
|
|
cstrittmatter@0
|
349 list_ids, searched_fastq_files = get_list_ids(workdir, args.listIDs.name if args.listIDs is not None else None,
|
|
cstrittmatter@0
|
350 args.taxon)
|
|
cstrittmatter@0
|
351
|
|
cstrittmatter@0
|
352 mlst_sequences = None
|
|
cstrittmatter@0
|
353 mlst_dicts = None
|
|
cstrittmatter@0
|
354 if args.mlst is not None:
|
|
cstrittmatter@0
|
355 time_taken_pub_mlst, mlst_dicts, mlst_sequences = check_mlst.download_pub_mlst_xml(args.mlst,
|
|
cstrittmatter@0
|
356 args.mlstSchemaNumber,
|
|
cstrittmatter@0
|
357 workdir)
|
|
cstrittmatter@0
|
358 args.softClip_recodeRun = 'first'
|
|
cstrittmatter@0
|
359
|
|
cstrittmatter@0
|
360 if args.reference is None:
|
|
cstrittmatter@0
|
361 if args.mlst is not None:
|
|
cstrittmatter@0
|
362 reference_file = check_mlst.check_existing_schema(args.mlst, args.mlstSchemaNumber, script_path)
|
|
cstrittmatter@0
|
363 args.extraSeq = 200
|
|
cstrittmatter@0
|
364 if reference_file is None:
|
|
cstrittmatter@0
|
365 print('It was not found provided MLST scheme sequences for ' + args.mlst)
|
|
cstrittmatter@0
|
366 print('Trying to obtain reference MLST sequences from PubMLST')
|
|
cstrittmatter@0
|
367 if len(mlst_sequences) > 0:
|
|
cstrittmatter@0
|
368 reference_file = check_mlst.write_mlst_reference(args.mlst, mlst_sequences, workdir, time_str)
|
|
cstrittmatter@0
|
369 args.extraSeq = 0
|
|
cstrittmatter@0
|
370 else:
|
|
cstrittmatter@0
|
371 sys.exit('It was not possible to download MLST sequences from PubMLST!')
|
|
cstrittmatter@0
|
372 else:
|
|
cstrittmatter@0
|
373 print('Using provided scheme as referece: ' + reference_file)
|
|
cstrittmatter@0
|
374 else:
|
|
cstrittmatter@0
|
375 sys.exit('Need to provide at least one of the following options: "--reference" and "--mlst"')
|
|
cstrittmatter@0
|
376 else:
|
|
cstrittmatter@0
|
377 reference_file = os.path.abspath(args.reference.name)
|
|
cstrittmatter@0
|
378
|
|
cstrittmatter@0
|
379 # Run ReMatCh for each sample
|
|
cstrittmatter@0
|
380 print('\n' + 'STARTING ReMatCh' + '\n')
|
|
cstrittmatter@0
|
381
|
|
cstrittmatter@0
|
382 # Clean sequences headers
|
|
cstrittmatter@0
|
383 reference_file, gene_list_reference, reference_dict = clean_headers_reference_file(reference_file, workdir,
|
|
cstrittmatter@0
|
384 args.extraSeq)
|
|
cstrittmatter@0
|
385
|
|
cstrittmatter@0
|
386 if args.mlst is not None:
|
|
cstrittmatter@0
|
387 problem_genes = False
|
|
cstrittmatter@0
|
388 for header in mlst_sequences:
|
|
cstrittmatter@0
|
389 if header not in gene_list_reference:
|
|
cstrittmatter@0
|
390 print('MLST gene {header} not found between reference sequences'.format(header=header))
|
|
cstrittmatter@0
|
391 problem_genes = True
|
|
cstrittmatter@0
|
392 if problem_genes:
|
|
cstrittmatter@0
|
393 sys.exit('Missing MLST genes from reference sequences (at least sequences names do not match)!')
|
|
cstrittmatter@0
|
394
|
|
cstrittmatter@0
|
395 if len(gene_list_reference) == 0:
|
|
cstrittmatter@0
|
396 sys.exit('No sequences left')
|
|
cstrittmatter@0
|
397
|
|
cstrittmatter@0
|
398 # To use in combined report
|
|
cstrittmatter@0
|
399
|
|
cstrittmatter@0
|
400 number_samples_successfully = 0
|
|
cstrittmatter@0
|
401 genes_present_coverage_depth = {}
|
|
cstrittmatter@0
|
402 genes_present_sequence_coverage = {}
|
|
cstrittmatter@0
|
403 for sample in list_ids:
|
|
cstrittmatter@0
|
404 sample_start_time = time.time()
|
|
cstrittmatter@0
|
405 print('\n\n' + 'Sample ID: ' + sample)
|
|
cstrittmatter@0
|
406
|
|
cstrittmatter@0
|
407 # Create sample outdir
|
|
cstrittmatter@0
|
408 sample_outdir = os.path.join(workdir, sample, '')
|
|
cstrittmatter@0
|
409 if not os.path.isdir(sample_outdir):
|
|
cstrittmatter@0
|
410 os.mkdir(sample_outdir)
|
|
cstrittmatter@0
|
411
|
|
cstrittmatter@0
|
412 run_successfully_fastq = None
|
|
cstrittmatter@0
|
413 time_taken_fastq = 0
|
|
cstrittmatter@0
|
414 sequencing_information = {'run_accession': None, 'instrument_platform': None, 'instrument_model': None,
|
|
cstrittmatter@0
|
415 'library_layout': None, 'library_source': None, 'extra_run_accession': None,
|
|
cstrittmatter@0
|
416 'nominal_length': None, 'read_count': None, 'base_count': None, 'date_download': None}
|
|
cstrittmatter@0
|
417 if not searched_fastq_files:
|
|
cstrittmatter@0
|
418 # Download Files
|
|
cstrittmatter@0
|
419 time_taken_fastq, run_successfully_fastq, fastq_files, sequencing_information = \
|
|
cstrittmatter@0
|
420 download.run_download(sample, args.downloadLibrariesType, aspera_key, sample_outdir,
|
|
cstrittmatter@0
|
421 args.downloadCramBam, args.threads, args.downloadInstrumentPlatform, args.SRA,
|
|
cstrittmatter@0
|
422 args.SRAopt)
|
|
cstrittmatter@0
|
423 else:
|
|
cstrittmatter@0
|
424 fastq_files = list_ids[sample]
|
|
cstrittmatter@0
|
425
|
|
cstrittmatter@0
|
426 file_size = None
|
|
cstrittmatter@0
|
427
|
|
cstrittmatter@0
|
428 run_successfully_rematch_first = None
|
|
cstrittmatter@0
|
429 run_successfully_rematch_second = None
|
|
cstrittmatter@0
|
430 time_taken_rematch_first = 0
|
|
cstrittmatter@0
|
431 time_taken_rematch_second = 0
|
|
cstrittmatter@0
|
432 sample_data_general_first = None
|
|
cstrittmatter@0
|
433 sample_data_general_second = None
|
|
cstrittmatter@0
|
434 if run_successfully_fastq is not False:
|
|
cstrittmatter@0
|
435 file_size = sum(os.path.getsize(fastq) for fastq in fastq_files)
|
|
cstrittmatter@0
|
436 # Run ReMatCh
|
|
cstrittmatter@0
|
437 time_taken_rematch_first, run_successfully_rematch_first, data_by_gene, sample_data_general_first, \
|
|
cstrittmatter@0
|
438 consensus_files, consensus_sequences = \
|
|
cstrittmatter@0
|
439 rematch_module.run_rematch_module(sample, fastq_files, reference_file, args.threads, sample_outdir,
|
|
cstrittmatter@0
|
440 args.extraSeq, args.minCovPresence, args.minCovCall,
|
|
cstrittmatter@0
|
441 args.minFrequencyDominantAllele, args.minGeneCoverage,
|
|
cstrittmatter@0
|
442 args.debug, args.numMapLoc, args.minGeneIdentity,
|
|
cstrittmatter@0
|
443 'first', args.softClip_baseQuality, args.softClip_recodeRun,
|
|
cstrittmatter@0
|
444 reference_dict, args.softClip_cigarFlagRecode,
|
|
cstrittmatter@0
|
445 args.bowtieAlgo, args.bowtieOPT,
|
|
cstrittmatter@0
|
446 gene_list_reference, args.notWriteConsensus, clean_run=True)
|
|
cstrittmatter@0
|
447 if run_successfully_rematch_first:
|
|
cstrittmatter@0
|
448 if args.mlst is not None and (args.mlstRun == 'first' or args.mlstRun == 'all'):
|
|
cstrittmatter@0
|
449 run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'first', workdir, time_str)
|
|
cstrittmatter@0
|
450 genes_present_coverage_depth = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
|
|
cstrittmatter@0
|
451 data_by_gene, workdir, time_str, 'first_run',
|
|
cstrittmatter@0
|
452 args.minGeneIdentity, 'coverage_depth', args.summary,
|
|
cstrittmatter@0
|
453 genes_present_coverage_depth)
|
|
cstrittmatter@0
|
454 if args.reportSequenceCoverage:
|
|
cstrittmatter@0
|
455 genes_present_sequence_coverage = write_data_by_gene(gene_list_reference, args.minGeneCoverage,
|
|
cstrittmatter@0
|
456 sample, data_by_gene, workdir, time_str,
|
|
cstrittmatter@0
|
457 'first_run', args.minGeneIdentity,
|
|
cstrittmatter@0
|
458 'sequence_coverage', args.summary,
|
|
cstrittmatter@0
|
459 genes_present_sequence_coverage)
|
|
cstrittmatter@0
|
460 if args.doubleRun:
|
|
cstrittmatter@0
|
461 rematch_second_outdir = os.path.join(sample_outdir, 'rematch_second_run', '')
|
|
cstrittmatter@0
|
462 if not os.path.isdir(rematch_second_outdir):
|
|
cstrittmatter@0
|
463 os.mkdir(rematch_second_outdir)
|
|
cstrittmatter@0
|
464 consensus_concatenated_fasta, consensus_concatenated_gene_list, consensus_concatenated_dict, \
|
|
cstrittmatter@0
|
465 number_consensus_with_sequences = \
|
|
cstrittmatter@0
|
466 concatenate_extra_seq_2_consensus(consensus_files['noMatter'], reference_file, args.extraSeq,
|
|
cstrittmatter@0
|
467 rematch_second_outdir)
|
|
cstrittmatter@0
|
468 if len(consensus_concatenated_gene_list) > 0:
|
|
cstrittmatter@0
|
469 if args.mlst is None or \
|
|
cstrittmatter@0
|
470 (args.mlst is not None and number_consensus_with_sequences == len(gene_list_reference)):
|
|
cstrittmatter@0
|
471 time_taken_rematch_second, run_successfully_rematch_second, data_by_gene, \
|
|
cstrittmatter@0
|
472 sample_data_general_second, consensus_files, consensus_sequences = \
|
|
cstrittmatter@0
|
473 rematch_module.run_rematch_module(sample, fastq_files, consensus_concatenated_fasta,
|
|
cstrittmatter@0
|
474 args.threads, rematch_second_outdir, args.extraSeq,
|
|
cstrittmatter@0
|
475 args.minCovPresence, args.minCovCall,
|
|
cstrittmatter@0
|
476 args.minFrequencyDominantAllele, args.minGeneCoverage,
|
|
cstrittmatter@0
|
477 args.debug, args.numMapLoc,
|
|
cstrittmatter@0
|
478 args.minGeneIdentity, 'second',
|
|
cstrittmatter@0
|
479 args.softClip_baseQuality, args.softClip_recodeRun,
|
|
cstrittmatter@0
|
480 consensus_concatenated_dict,
|
|
cstrittmatter@0
|
481 args.softClip_cigarFlagRecode,
|
|
cstrittmatter@0
|
482 args.bowtieAlgo, args.bowtieOPT,
|
|
cstrittmatter@0
|
483 gene_list_reference, args.notWriteConsensus,
|
|
cstrittmatter@0
|
484 clean_run=True)
|
|
cstrittmatter@0
|
485 if not args.debug:
|
|
cstrittmatter@0
|
486 os.remove(consensus_concatenated_fasta)
|
|
cstrittmatter@0
|
487 if run_successfully_rematch_second:
|
|
cstrittmatter@0
|
488 if args.mlst is not None and (args.mlstRun == 'second' or args.mlstRun == 'all'):
|
|
cstrittmatter@0
|
489 run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'second',
|
|
cstrittmatter@0
|
490 workdir, time_str)
|
|
cstrittmatter@0
|
491 _ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample, data_by_gene,
|
|
cstrittmatter@0
|
492 workdir, time_str, 'second_run', args.minGeneIdentity,
|
|
cstrittmatter@0
|
493 'coverage_depth', False, {})
|
|
cstrittmatter@0
|
494 if args.reportSequenceCoverage:
|
|
cstrittmatter@0
|
495 _ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
|
|
cstrittmatter@0
|
496 data_by_gene, workdir, time_str, 'second_run',
|
|
cstrittmatter@0
|
497 args.minGeneIdentity, 'sequence_coverage', False, {})
|
|
cstrittmatter@0
|
498 else:
|
|
cstrittmatter@0
|
499 print('Some sequences missing after ReMatCh module first run. Second run will not be'
|
|
cstrittmatter@0
|
500 ' performed')
|
|
cstrittmatter@0
|
501 if os.path.isfile(consensus_concatenated_fasta):
|
|
cstrittmatter@0
|
502 os.remove(consensus_concatenated_fasta)
|
|
cstrittmatter@0
|
503 if os.path.isdir(rematch_second_outdir):
|
|
cstrittmatter@0
|
504 utils.remove_directory(rematch_second_outdir)
|
|
cstrittmatter@0
|
505 else:
|
|
cstrittmatter@0
|
506 print('No sequences left after ReMatCh module first run. Second run will not be performed')
|
|
cstrittmatter@0
|
507 if os.path.isfile(consensus_concatenated_fasta):
|
|
cstrittmatter@0
|
508 os.remove(consensus_concatenated_fasta)
|
|
cstrittmatter@0
|
509 if os.path.isdir(rematch_second_outdir):
|
|
cstrittmatter@0
|
510 utils.remove_directory(rematch_second_outdir)
|
|
cstrittmatter@0
|
511
|
|
cstrittmatter@0
|
512 if not searched_fastq_files and not args.keepDownloadedFastq and fastq_files is not None:
|
|
cstrittmatter@0
|
513 for fastq in fastq_files:
|
|
cstrittmatter@0
|
514 if os.path.isfile(fastq):
|
|
cstrittmatter@0
|
515 os.remove(fastq)
|
|
cstrittmatter@0
|
516
|
|
cstrittmatter@0
|
517 time_taken = utils.run_time(sample_start_time)
|
|
cstrittmatter@0
|
518
|
|
cstrittmatter@0
|
519 write_sample_report(sample, workdir, time_str, file_size, run_successfully_fastq,
|
|
cstrittmatter@0
|
520 run_successfully_rematch_first, run_successfully_rematch_second, time_taken_fastq,
|
|
cstrittmatter@0
|
521 time_taken_rematch_first, time_taken_rematch_second, time_taken, sequencing_information,
|
|
cstrittmatter@0
|
522 sample_data_general_first if run_successfully_rematch_first else
|
|
cstrittmatter@0
|
523 {'number_absent_genes': None, 'number_genes_multiple_alleles': None,
|
|
cstrittmatter@0
|
524 'mean_sample_coverage': None},
|
|
cstrittmatter@0
|
525 sample_data_general_second if run_successfully_rematch_second else
|
|
cstrittmatter@0
|
526 {'number_absent_genes': None, 'number_genes_multiple_alleles': None,
|
|
cstrittmatter@0
|
527 'mean_sample_coverage': None},
|
|
cstrittmatter@0
|
528 fastq_files if fastq_files is not None else '')
|
|
cstrittmatter@0
|
529
|
|
cstrittmatter@0
|
530 if all([run_successfully_fastq is not False,
|
|
cstrittmatter@0
|
531 run_successfully_rematch_first is not False,
|
|
cstrittmatter@0
|
532 run_successfully_rematch_second is not False]):
|
|
cstrittmatter@0
|
533 number_samples_successfully += 1
|
|
cstrittmatter@0
|
534
|
|
cstrittmatter@0
|
535 if args.summary:
|
|
cstrittmatter@0
|
536 write_summary_report(workdir, 'coverage_depth', time_str, gene_list_reference, genes_present_coverage_depth)
|
|
cstrittmatter@0
|
537 if args.reportSequenceCoverage:
|
|
cstrittmatter@0
|
538 write_summary_report(workdir, 'sequence_coverage', time_str, gene_list_reference,
|
|
cstrittmatter@0
|
539 genes_present_sequence_coverage)
|
|
cstrittmatter@0
|
540
|
|
cstrittmatter@0
|
541 return number_samples_successfully, len(list_ids)
|
|
cstrittmatter@0
|
542
|
|
cstrittmatter@0
|
543
|
|
cstrittmatter@0
|
544 def main():
|
|
cstrittmatter@0
|
545 if sys.version_info[0] < 3:
|
|
cstrittmatter@0
|
546 sys.exit('Must be using Python 3. Try calling "python3 rematch.py"')
|
|
cstrittmatter@0
|
547
|
|
cstrittmatter@0
|
548 parser = argparse.ArgumentParser(prog='rematch.py',
|
|
cstrittmatter@0
|
549 description='Reads mapping against target sequences, checking mapping and'
|
|
cstrittmatter@0
|
550 ' consensus sequences production',
|
|
cstrittmatter@0
|
551 formatter_class=argparse.ArgumentDefaultsHelpFormatter)
|
|
cstrittmatter@0
|
552 parser.add_argument('--version', help='Version information', action='version',
|
|
cstrittmatter@0
|
553 version='{prog} v{version}'.format(prog=parser.prog, version=__version__))
|
|
cstrittmatter@0
|
554
|
|
cstrittmatter@0
|
555 parser_optional_general = parser.add_argument_group('General facultative options')
|
|
cstrittmatter@0
|
556 parser_optional_general.add_argument('-r', '--reference', type=argparse.FileType('r'),
|
|
cstrittmatter@0
|
557 metavar='/path/to/reference_sequence.fasta',
|
|
cstrittmatter@0
|
558 help='Fasta file containing reference sequences', required=False)
|
|
cstrittmatter@0
|
559 parser_optional_general.add_argument('-w', '--workdir', type=str, metavar='/path/to/workdir/directory/',
|
|
cstrittmatter@0
|
560 help='Path to the directory where ReMatCh will run and produce the outputs'
|
|
cstrittmatter@0
|
561 ' with reads (ended with fastq.gz/fq.gz and, in case of PE data, pair-end'
|
|
cstrittmatter@0
|
562 ' direction coded as _R1_001 / _R2_001 or _1 / _2) already'
|
|
cstrittmatter@0
|
563 ' present (organized in sample folders) or to be downloaded',
|
|
cstrittmatter@0
|
564 required=False, default='.')
|
|
cstrittmatter@0
|
565 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use',
|
|
cstrittmatter@0
|
566 required=False, default=1)
|
|
cstrittmatter@0
|
567 parser_optional_general.add_argument('--mlst', type=str, metavar='"Streptococcus agalactiae"',
|
|
cstrittmatter@0
|
568 help='Species name (same as in PubMLST) to be used in MLST'
|
|
cstrittmatter@0
|
569 ' determination. ReMatCh will use Bowtie2 very-sensitive-local mapping'
|
|
cstrittmatter@0
|
570 ' parameters and will recode the soft clip CIGAR flags of the first run',
|
|
cstrittmatter@0
|
571 required=False)
|
|
cstrittmatter@0
|
572 parser_optional_general.add_argument('--doNotUseProvidedSoftware', action='store_true',
|
|
cstrittmatter@0
|
573 help='Tells ReMatCh to not use Bowtie2, Samtools and Bcftools that are'
|
|
cstrittmatter@0
|
574 ' provided with it')
|
|
cstrittmatter@0
|
575
|
|
cstrittmatter@0
|
576 parser_optional_download_exclusive = parser.add_mutually_exclusive_group()
|
|
cstrittmatter@0
|
577 parser_optional_download_exclusive.add_argument('-l', '--listIDs', type=argparse.FileType('r'),
|
|
cstrittmatter@0
|
578 metavar='/path/to/list_IDs.txt',
|
|
cstrittmatter@0
|
579 help='Path to list containing the IDs to be'
|
|
cstrittmatter@0
|
580 ' downloaded (one per line)', required=False)
|
|
cstrittmatter@0
|
581 parser_optional_download_exclusive.add_argument('-t', '--taxon', type=str, metavar='"Streptococcus agalactiae"',
|
|
cstrittmatter@0
|
582 help='Taxon name for which ReMatCh will download fastq files',
|
|
cstrittmatter@0
|
583 required=False)
|
|
cstrittmatter@0
|
584
|
|
cstrittmatter@0
|
585 parser_optional_rematch = parser.add_argument_group('ReMatCh module facultative options')
|
|
cstrittmatter@0
|
586 parser_optional_rematch.add_argument('--extraSeq', type=int, metavar='N',
|
|
cstrittmatter@0
|
587 help='Sequence length added to both ends of target sequences (usefull to'
|
|
cstrittmatter@0
|
588 ' improve reads mapping to the target one) that will be trimmed in'
|
|
cstrittmatter@0
|
589 ' ReMatCh outputs', required=False, default=0)
|
|
cstrittmatter@0
|
590 parser_optional_rematch.add_argument('--minCovPresence', type=int, metavar='N',
|
|
cstrittmatter@0
|
591 help='Reference position minimum coverage depth to consider the position to be'
|
|
cstrittmatter@0
|
592 ' present in the sample', required=False, default=5)
|
|
cstrittmatter@0
|
593 parser_optional_rematch.add_argument('--minCovCall', type=int, metavar='N',
|
|
cstrittmatter@0
|
594 help='Reference position minimum coverage depth to perform a base call. Lower'
|
|
cstrittmatter@0
|
595 ' coverage will be coded as N', required=False, default=10)
|
|
cstrittmatter@0
|
596 parser_optional_rematch.add_argument('--minFrequencyDominantAllele', type=float, metavar='0.6',
|
|
cstrittmatter@0
|
597 help='Minimum relative frequency of the dominant allele coverage depth (value'
|
|
cstrittmatter@0
|
598 ' between [0, 1]). Positions with lower values will be considered as'
|
|
cstrittmatter@0
|
599 ' having multiple alleles (and will be coded as N)', required=False,
|
|
cstrittmatter@0
|
600 default=0.6)
|
|
cstrittmatter@0
|
601 parser_optional_rematch.add_argument('--minGeneCoverage', type=int, metavar='N',
|
|
cstrittmatter@0
|
602 help='Minimum percentage of target reference gene sequence covered'
|
|
cstrittmatter@0
|
603 ' by --minCovPresence to consider a gene to be present (value'
|
|
cstrittmatter@0
|
604 ' between [0, 100])', required=False, default=70)
|
|
cstrittmatter@0
|
605 parser_optional_rematch.add_argument('--minGeneIdentity', type=int, metavar='N',
|
|
cstrittmatter@0
|
606 help='Minimum percentage of identity of reference gene sequence covered'
|
|
cstrittmatter@0
|
607 ' by --minCovCall to consider a gene to be present (value'
|
|
cstrittmatter@0
|
608 ' between [0, 100]). One INDEL will be considered as one difference',
|
|
cstrittmatter@0
|
609 required=False, default=80)
|
|
cstrittmatter@0
|
610 parser_optional_rematch.add_argument('--numMapLoc', type=int, metavar='N', help=argparse.SUPPRESS, required=False,
|
|
cstrittmatter@0
|
611 default=1)
|
|
cstrittmatter@0
|
612 # parser_optional_rematch.add_argument('--numMapLoc', type=int, metavar='N', help='Maximum number of locations to which a read can map (sometimes useful when mapping against similar sequences)', required=False, default=1)
|
|
cstrittmatter@0
|
613 parser_optional_rematch.add_argument('--doubleRun', action='store_true',
|
|
cstrittmatter@0
|
614 help='Tells ReMatCh to run a second time using as reference the noMatter'
|
|
cstrittmatter@0
|
615 ' consensus sequence produced in the first run. This will improve'
|
|
cstrittmatter@0
|
616 ' consensus sequence determination for sequences with high percentage of'
|
|
cstrittmatter@0
|
617 ' target reference gene sequence covered')
|
|
cstrittmatter@0
|
618 parser_optional_rematch.add_argument('--reportSequenceCoverage', action='store_true',
|
|
cstrittmatter@0
|
619 help='Produce an extra combined_report.data_by_gene with the sequence coverage'
|
|
cstrittmatter@0
|
620 ' instead of coverage depth')
|
|
cstrittmatter@0
|
621 parser_optional_rematch.add_argument('--summary', action='store_true',
|
|
cstrittmatter@0
|
622 help='Produce extra report files containing only sequences present in at least'
|
|
cstrittmatter@0
|
623 ' one sample (usefull when using a large number of reference'
|
|
cstrittmatter@0
|
624 ' sequences, and only for first run)')
|
|
cstrittmatter@0
|
625 parser_optional_rematch.add_argument('--notWriteConsensus', action='store_true',
|
|
cstrittmatter@0
|
626 help='Do not write consensus sequences')
|
|
cstrittmatter@0
|
627 parser_optional_rematch.add_argument('--bowtieAlgo', type=str, metavar='"--very-sensitive-local"',
|
|
cstrittmatter@0
|
628 help='Bowtie2 alignment mode. It can be an end-to-end alignment (unclipped'
|
|
cstrittmatter@0
|
629 ' alignment) or local alignment (soft clipped alignment). Also, can'
|
|
cstrittmatter@0
|
630 ' choose between fast or sensitive alignments. Please check Bowtie2'
|
|
cstrittmatter@0
|
631 ' manual for extra'
|
|
cstrittmatter@0
|
632 ' information: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml .'
|
|
cstrittmatter@0
|
633 ' This option should be provided between quotes and starting with'
|
|
cstrittmatter@0
|
634 ' an empty space (like --bowtieAlgo " --very-fast") or using equal'
|
|
cstrittmatter@0
|
635 ' sign (like --bowtieAlgo="--very-fast")',
|
|
cstrittmatter@0
|
636 required=False, default='--very-sensitive-local')
|
|
cstrittmatter@0
|
637 parser_optional_rematch.add_argument('--bowtieOPT', type=str, metavar='"--no-mixed"',
|
|
cstrittmatter@0
|
638 help='Extra Bowtie2 options. This option should be provided between quotes and'
|
|
cstrittmatter@0
|
639 ' starting with an empty space (like --bowtieOPT " --no-mixed") or using'
|
|
cstrittmatter@0
|
640 ' equal sign (like --bowtieOPT="--no-mixed")',
|
|
cstrittmatter@0
|
641 required=False)
|
|
cstrittmatter@0
|
642 parser_optional_rematch.add_argument('--debug', action='store_true',
|
|
cstrittmatter@0
|
643 help='DeBug Mode: do not remove temporary files')
|
|
cstrittmatter@0
|
644
|
|
cstrittmatter@0
|
645 parser_optional_mlst = parser.add_argument_group('MLST facultative options')
|
|
cstrittmatter@0
|
646 parser_optional_rematch.add_argument('--mlstReference', action='store_true',
|
|
cstrittmatter@0
|
647 help='If the curated scheme for MLST alleles is available, tells ReMatCh to'
|
|
cstrittmatter@0
|
648 ' use these as reference (force Bowtie2 to run with very-sensitive-local'
|
|
cstrittmatter@0
|
649 ' parameters, and sets --extraSeq to 200), otherwise ReMatCh uses the'
|
|
cstrittmatter@0
|
650 ' first alleles of each MLST gene fragment in PubMLST as reference'
|
|
cstrittmatter@0
|
651 ' sequences (force Bowtie2 to run with very-sensitive-local parameters,'
|
|
cstrittmatter@0
|
652 ' and sets --extraSeq to 0)')
|
|
cstrittmatter@0
|
653 parser_optional_mlst.add_argument('--mlstSchemaNumber', type=int, metavar='N',
|
|
cstrittmatter@0
|
654 help='Number of the species PubMLST schema to be used in case of multiple schemes'
|
|
cstrittmatter@0
|
655 ' available (by default will use the first schema)', required=False)
|
|
cstrittmatter@0
|
656 parser_optional_mlst.add_argument('--mlstConsensus', choices=['noMatter', 'correct', 'alignment', 'all'], type=str,
|
|
cstrittmatter@0
|
657 metavar='noMatter',
|
|
cstrittmatter@0
|
658 help='Consensus sequence to be used in MLST'
|
|
cstrittmatter@0
|
659 ' determination (available options: %(choices)s)', required=False,
|
|
cstrittmatter@0
|
660 default='noMatter')
|
|
cstrittmatter@0
|
661 parser_optional_mlst.add_argument('--mlstRun', choices=['first', 'second', 'all'], type=str, metavar='first',
|
|
cstrittmatter@0
|
662 help='ReMatCh run outputs to be used in MLST determination (available'
|
|
cstrittmatter@0
|
663 ' options: %(choices)s)', required=False, default='all')
|
|
cstrittmatter@0
|
664
|
|
cstrittmatter@0
|
665 parser_optional_download = parser.add_argument_group('Download facultative options')
|
|
cstrittmatter@0
|
666 parser_optional_download.add_argument('-a', '--asperaKey', type=argparse.FileType('r'),
|
|
cstrittmatter@0
|
667 metavar='/path/to/asperaweb_id_dsa.openssh',
|
|
cstrittmatter@0
|
668 help='Tells ReMatCh to download fastq files from ENA using Aspera'
|
|
cstrittmatter@0
|
669 ' Connect. With this option, the path to Private-key file'
|
|
cstrittmatter@0
|
670 ' asperaweb_id_dsa.openssh must be provided (normaly found in'
|
|
cstrittmatter@0
|
671 ' ~/.aspera/connect/etc/asperaweb_id_dsa.openssh).', required=False)
|
|
cstrittmatter@0
|
672 parser_optional_download.add_argument('-k', '--keepDownloadedFastq', action='store_true',
|
|
cstrittmatter@0
|
673 help='Tells ReMatCh to keep the fastq files downloaded')
|
|
cstrittmatter@0
|
674 parser_optional_download.add_argument('--downloadLibrariesType', type=str, metavar='PAIRED',
|
|
cstrittmatter@0
|
675 help='Tells ReMatCh to download files with specific library'
|
|
cstrittmatter@0
|
676 ' layout (available options: %(choices)s)',
|
|
cstrittmatter@0
|
677 choices=['PAIRED', 'SINGLE', 'BOTH'], required=False, default='BOTH')
|
|
cstrittmatter@0
|
678 parser_optional_download.add_argument('--downloadInstrumentPlatform', type=str, metavar='ILLUMINA',
|
|
cstrittmatter@0
|
679 help='Tells ReMatCh to download files with specific library layout (available'
|
|
cstrittmatter@0
|
680 ' options: %(choices)s)', choices=['ILLUMINA', 'ALL'], required=False,
|
|
cstrittmatter@0
|
681 default='ILLUMINA')
|
|
cstrittmatter@0
|
682 parser_optional_download.add_argument('--downloadCramBam', action='store_true',
|
|
cstrittmatter@0
|
683 help='Tells ReMatCh to also download cram/bam files and convert them to fastq'
|
|
cstrittmatter@0
|
684 ' files')
|
|
cstrittmatter@0
|
685
|
|
cstrittmatter@0
|
686 parser_optional_sra = parser.add_mutually_exclusive_group()
|
|
cstrittmatter@0
|
687 parser_optional_sra.add_argument('--SRA', action='store_true',
|
|
cstrittmatter@0
|
688 help='Tells getSeqENA.py to download reads in fastq format only from NCBI SRA'
|
|
cstrittmatter@0
|
689 ' database (not recommended)')
|
|
cstrittmatter@0
|
690 parser_optional_sra.add_argument('--SRAopt', action='store_true',
|
|
cstrittmatter@0
|
691 help='Tells getSeqENA.py to download reads from NCBI SRA if the download from ENA'
|
|
cstrittmatter@0
|
692 ' fails')
|
|
cstrittmatter@0
|
693
|
|
cstrittmatter@0
|
694 parser_optional_soft_clip = parser.add_argument_group('Soft clip facultative options')
|
|
cstrittmatter@0
|
695 parser_optional_soft_clip.add_argument('--softClip_baseQuality', type=int, metavar='N',
|
|
cstrittmatter@0
|
696 help='Base quality phred score in reads soft clipped regions',
|
|
cstrittmatter@0
|
697 required=False,
|
|
cstrittmatter@0
|
698 default=7)
|
|
cstrittmatter@0
|
699 parser_optional_soft_clip.add_argument('--softClip_recodeRun', type=str, metavar='first',
|
|
cstrittmatter@0
|
700 help='ReMatCh run to recode soft clipped regions (available'
|
|
cstrittmatter@0
|
701 ' options: %(choices)s)', choices=['first', 'second', 'both', 'none'],
|
|
cstrittmatter@0
|
702 required=False, default='none')
|
|
cstrittmatter@0
|
703 parser_optional_soft_clip.add_argument('--softClip_cigarFlagRecode', type=str, metavar='M',
|
|
cstrittmatter@0
|
704 help='CIGAR flag to recode CIGAR soft clip (available options: %(choices)s)',
|
|
cstrittmatter@0
|
705 choices=['M', 'I', 'X'], required=False, default='X')
|
|
cstrittmatter@0
|
706
|
|
cstrittmatter@0
|
707 args = parser.parse_args()
|
|
cstrittmatter@0
|
708
|
|
cstrittmatter@0
|
709 msg = []
|
|
cstrittmatter@0
|
710 if args.reference is None and not args.mlstReference:
|
|
cstrittmatter@0
|
711 msg.append('At least --reference or --mlstReference should be provided')
|
|
cstrittmatter@0
|
712 elif args.reference is not None and args.mlstReference:
|
|
cstrittmatter@0
|
713 msg.append('Only --reference or --mlstReference should be provided')
|
|
cstrittmatter@0
|
714 else:
|
|
cstrittmatter@0
|
715 if args.mlstReference:
|
|
cstrittmatter@0
|
716 if args.mlst is None:
|
|
cstrittmatter@0
|
717 msg.append('Please provide species name using --mlst')
|
|
cstrittmatter@0
|
718 if args.minFrequencyDominantAllele < 0 or args.minFrequencyDominantAllele > 1:
|
|
cstrittmatter@0
|
719 msg.append('--minFrequencyDominantAllele should be a value between [0, 1]')
|
|
cstrittmatter@0
|
720 if args.minGeneCoverage < 0 or args.minGeneCoverage > 100:
|
|
cstrittmatter@0
|
721 msg.append('--minGeneCoverage should be a value between [0, 100]')
|
|
cstrittmatter@0
|
722 if args.minGeneIdentity < 0 or args.minGeneIdentity > 100:
|
|
cstrittmatter@0
|
723 msg.append('--minGeneIdentity should be a value between [0, 100]')
|
|
cstrittmatter@0
|
724 if args.notWriteConsensus and args.doubleRun:
|
|
cstrittmatter@0
|
725 msg.append('--notWriteConsensus and --doubleRun cannot be used together.'
|
|
cstrittmatter@0
|
726 ' Maybe you only want to use --doubleRun')
|
|
cstrittmatter@0
|
727
|
|
cstrittmatter@0
|
728 if len(msg) > 0:
|
|
cstrittmatter@0
|
729 argparse.ArgumentParser.error('\n'.join(msg))
|
|
cstrittmatter@0
|
730
|
|
cstrittmatter@0
|
731 start_time = time.time()
|
|
cstrittmatter@0
|
732
|
|
cstrittmatter@0
|
733 number_samples_successfully, samples_total_number = run_rematch(args)
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|
cstrittmatter@0
|
734
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cstrittmatter@0
|
735 print('\n' + 'END ReMatCh')
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|
cstrittmatter@0
|
736 print('\n' +
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|
cstrittmatter@0
|
737 str(number_samples_successfully) + ' samples out of ' + str(samples_total_number) + ' run successfully')
|
|
cstrittmatter@0
|
738 time_taken = utils.run_time(start_time)
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|
cstrittmatter@0
|
739 del time_taken
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|
cstrittmatter@0
|
740
|
|
cstrittmatter@0
|
741 if number_samples_successfully == 0:
|
|
cstrittmatter@0
|
742 sys.exit('No samples run successfully!')
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|
cstrittmatter@0
|
743
|
|
cstrittmatter@0
|
744
|
|
cstrittmatter@0
|
745 if __name__ == "__main__":
|
|
cstrittmatter@0
|
746 main()
|
