annotate scripts/ReMatCh/rematch.py @ 6:20ff3dca457f draft default tip

planemo upload commit 6857c749c21f580c828aba3543e294b69d32b662
author iss
date Mon, 23 Oct 2023 11:45:36 +0000
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children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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')
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264 with open(consensus_concatenated, 'wt') as writer:
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265 for i in consensus_dict:
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266 writer.write('>' + consensus_dict[i]['header'] + '\n')
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267 fasta_sequence_lines = rematch_module.chunkstring(consensus_dict[i]['sequence'], 80)
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268 for line in fasta_sequence_lines:
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269 writer.write(line + '\n')
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270
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271 return consensus_concatenated, genes, consensus_dict, number_consensus_with_sequences
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272
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273
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274 def clean_headers_reference_file(reference_file, outdir, extra_seq):
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275 problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
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276 print('Checking if reference sequences contain ' + str(problematic_characters) + '\n')
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277 # headers_changed = False
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278 new_reference_file = str(reference_file)
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279 sequences, genes, headers_changed = rematch_module.get_sequence_information(reference_file, extra_seq)
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280 if headers_changed:
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281 print('At least one of the those characters was found. Replacing those with _' + '\n')
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282 new_reference_file = \
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283 os.path.join(outdir, os.path.splitext(os.path.basename(reference_file))[0] + '.headers_renamed.fasta')
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284 with open(new_reference_file, 'wt') as writer:
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285 for i in sequences:
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286 writer.write('>' + sequences[i]['header'] + '\n')
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287 fasta_sequence_lines = rematch_module.chunkstring(sequences[i]['sequence'], 80)
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288 for line in fasta_sequence_lines:
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289 writer.write(line + '\n')
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290 return new_reference_file, genes, sequences
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291
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292
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293 def write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, loci_order, outdir, time_str):
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294 mlst_report = os.path.join(outdir, 'mlst_report.' + time_str + '.tab')
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295 mlst_report_exist = os.path.isfile(mlst_report)
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296 with open(mlst_report, 'at') as writer:
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297 if not mlst_report_exist:
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298 writer.write('\t'.join(['#sample', 'ReMatCh_run', 'consensus_type', 'ST'] + loci_order) + '\n')
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299 writer.write('\t'.join([sample, run_times, consensus_type, str(st)] + alleles_profile.split(',')) + '\n')
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300
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301
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302 def run_get_st(sample, mlst_dicts, consensus_sequences, mlst_consensus, run_times, outdir, time_str):
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303 if mlst_consensus == 'all':
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304 for consensus_type in consensus_sequences:
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305 print('Searching MLST for ' + consensus_type + ' consensus')
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306 st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[consensus_type])
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307 write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, mlst_dicts[2], outdir, time_str)
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308 print('ST found: ' + str(st) + ' (' + alleles_profile + ')')
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309 else:
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310 st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[mlst_consensus])
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311 write_mlst_report(sample, run_times, mlst_consensus, st, alleles_profile, mlst_dicts[2], outdir, time_str)
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312 print('ST found for ' + mlst_consensus + ' consensus: ' + str(st) + ' (' + alleles_profile + ')')
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313
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314
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315 def write_summary_report(outdir, reported_data_type, time_str, gene_list_reference, genes_present):
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316 with open(os.path.join(outdir,
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317 'summary.{reported_data_type}.{time_str}.tab'.format(reported_data_type=reported_data_type,
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318 time_str=time_str)), 'wt') as writer:
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319 seq_list = []
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320 for info in list(genes_present.values()):
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321 seq_list.extend(list(info.keys()))
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322 seq_list = list(set(seq_list))
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323 writer.write('#sample' + '\t' + '\t'.join([gene_list_reference[seq] for seq in sorted(seq_list)]) + '\n')
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324 for sample, info in list(genes_present.items()):
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325 data = []
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326 for seq in sorted(seq_list):
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327 if seq in info:
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328 data.append(info[seq])
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329 else:
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330 data.append('NF')
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331 writer.write(sample + '\t' + '\t'.join(data) + '\n')
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332
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333
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334 def run_rematch(args):
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335 workdir = os.path.abspath(args.workdir)
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336 if not os.path.isdir(workdir):
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337 os.makedirs(workdir)
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338
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339 aspera_key = os.path.abspath(args.asperaKey.name) if args.asperaKey is not None else None
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340
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341 # Start logger
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342 logfile, time_str = utils.start_logger(workdir)
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343
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344 # Get general information
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345 script_path = utils.general_information(logfile, __version__, workdir, time_str, args.doNotUseProvidedSoftware,
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346 aspera_key, args.downloadCramBam, args.SRA, args.SRAopt)
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347
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348 # Set list_ids
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349 list_ids, searched_fastq_files = get_list_ids(workdir, args.listIDs.name if args.listIDs is not None else None,
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350 args.taxon)
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351
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352 mlst_sequences = None
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353 mlst_dicts = None
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354 if args.mlst is not None:
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355 time_taken_pub_mlst, mlst_dicts, mlst_sequences = check_mlst.download_pub_mlst_xml(args.mlst,
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356 args.mlstSchemaNumber,
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357 workdir)
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358 args.softClip_recodeRun = 'first'
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359
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360 if args.reference is None:
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361 if args.mlst is not None:
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362 reference_file = check_mlst.check_existing_schema(args.mlst, args.mlstSchemaNumber, script_path)
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363 args.extraSeq = 200
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364 if reference_file is None:
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365 print('It was not found provided MLST scheme sequences for ' + args.mlst)
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366 print('Trying to obtain reference MLST sequences from PubMLST')
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367 if len(mlst_sequences) > 0:
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368 reference_file = check_mlst.write_mlst_reference(args.mlst, mlst_sequences, workdir, time_str)
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369 args.extraSeq = 0
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370 else:
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371 sys.exit('It was not possible to download MLST sequences from PubMLST!')
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372 else:
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373 print('Using provided scheme as referece: ' + reference_file)
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374 else:
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375 sys.exit('Need to provide at least one of the following options: "--reference" and "--mlst"')
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376 else:
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377 reference_file = os.path.abspath(args.reference.name)
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378
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379 # Run ReMatCh for each sample
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380 print('\n' + 'STARTING ReMatCh' + '\n')
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381
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382 # Clean sequences headers
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383 reference_file, gene_list_reference, reference_dict = clean_headers_reference_file(reference_file, workdir,
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384 args.extraSeq)
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385
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386 if args.mlst is not None:
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387 problem_genes = False
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388 for header in mlst_sequences:
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389 if header not in gene_list_reference:
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390 print('MLST gene {header} not found between reference sequences'.format(header=header))
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391 problem_genes = True
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392 if problem_genes:
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393 sys.exit('Missing MLST genes from reference sequences (at least sequences names do not match)!')
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394
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395 if len(gene_list_reference) == 0:
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396 sys.exit('No sequences left')
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397
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398 # To use in combined report
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399
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400 number_samples_successfully = 0
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401 genes_present_coverage_depth = {}
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402 genes_present_sequence_coverage = {}
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403 for sample in list_ids:
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404 sample_start_time = time.time()
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405 print('\n\n' + 'Sample ID: ' + sample)
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406
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407 # Create sample outdir
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408 sample_outdir = os.path.join(workdir, sample, '')
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409 if not os.path.isdir(sample_outdir):
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410 os.mkdir(sample_outdir)
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411
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412 run_successfully_fastq = None
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413 time_taken_fastq = 0
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414 sequencing_information = {'run_accession': None, 'instrument_platform': None, 'instrument_model': None,
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415 'library_layout': None, 'library_source': None, 'extra_run_accession': None,
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416 'nominal_length': None, 'read_count': None, 'base_count': None, 'date_download': None}
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417 if not searched_fastq_files:
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418 # Download Files
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419 time_taken_fastq, run_successfully_fastq, fastq_files, sequencing_information = \
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420 download.run_download(sample, args.downloadLibrariesType, aspera_key, sample_outdir,
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421 args.downloadCramBam, args.threads, args.downloadInstrumentPlatform, args.SRA,
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422 args.SRAopt)
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423 else:
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424 fastq_files = list_ids[sample]
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425
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426 file_size = None
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427
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428 run_successfully_rematch_first = None
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429 run_successfully_rematch_second = None
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430 time_taken_rematch_first = 0
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431 time_taken_rematch_second = 0
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432 sample_data_general_first = None
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433 sample_data_general_second = None
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434 if run_successfully_fastq is not False:
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435 file_size = sum(os.path.getsize(fastq) for fastq in fastq_files)
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436 # Run ReMatCh
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437 time_taken_rematch_first, run_successfully_rematch_first, data_by_gene, sample_data_general_first, \
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438 consensus_files, consensus_sequences = \
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439 rematch_module.run_rematch_module(sample, fastq_files, reference_file, args.threads, sample_outdir,
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440 args.extraSeq, args.minCovPresence, args.minCovCall,
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441 args.minFrequencyDominantAllele, args.minGeneCoverage,
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442 args.debug, args.numMapLoc, args.minGeneIdentity,
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443 'first', args.softClip_baseQuality, args.softClip_recodeRun,
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444 reference_dict, args.softClip_cigarFlagRecode,
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445 args.bowtieAlgo, args.bowtieOPT,
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446 gene_list_reference, args.notWriteConsensus, clean_run=True)
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447 if run_successfully_rematch_first:
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448 if args.mlst is not None and (args.mlstRun == 'first' or args.mlstRun == 'all'):
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449 run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'first', workdir, time_str)
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450 genes_present_coverage_depth = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
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451 data_by_gene, workdir, time_str, 'first_run',
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452 args.minGeneIdentity, 'coverage_depth', args.summary,
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453 genes_present_coverage_depth)
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454 if args.reportSequenceCoverage:
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455 genes_present_sequence_coverage = write_data_by_gene(gene_list_reference, args.minGeneCoverage,
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456 sample, data_by_gene, workdir, time_str,
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457 'first_run', args.minGeneIdentity,
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458 'sequence_coverage', args.summary,
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459 genes_present_sequence_coverage)
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460 if args.doubleRun:
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461 rematch_second_outdir = os.path.join(sample_outdir, 'rematch_second_run', '')
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462 if not os.path.isdir(rematch_second_outdir):
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463 os.mkdir(rematch_second_outdir)
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464 consensus_concatenated_fasta, consensus_concatenated_gene_list, consensus_concatenated_dict, \
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465 number_consensus_with_sequences = \
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466 concatenate_extra_seq_2_consensus(consensus_files['noMatter'], reference_file, args.extraSeq,
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467 rematch_second_outdir)
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468 if len(consensus_concatenated_gene_list) > 0:
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469 if args.mlst is None or \
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470 (args.mlst is not None and number_consensus_with_sequences == len(gene_list_reference)):
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471 time_taken_rematch_second, run_successfully_rematch_second, data_by_gene, \
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472 sample_data_general_second, consensus_files, consensus_sequences = \
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473 rematch_module.run_rematch_module(sample, fastq_files, consensus_concatenated_fasta,
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474 args.threads, rematch_second_outdir, args.extraSeq,
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475 args.minCovPresence, args.minCovCall,
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476 args.minFrequencyDominantAllele, args.minGeneCoverage,
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477 args.debug, args.numMapLoc,
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478 args.minGeneIdentity, 'second',
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479 args.softClip_baseQuality, args.softClip_recodeRun,
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480 consensus_concatenated_dict,
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481 args.softClip_cigarFlagRecode,
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482 args.bowtieAlgo, args.bowtieOPT,
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483 gene_list_reference, args.notWriteConsensus,
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484 clean_run=True)
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485 if not args.debug:
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486 os.remove(consensus_concatenated_fasta)
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487 if run_successfully_rematch_second:
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488 if args.mlst is not None and (args.mlstRun == 'second' or args.mlstRun == 'all'):
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489 run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'second',
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490 workdir, time_str)
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491 _ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample, data_by_gene,
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492 workdir, time_str, 'second_run', args.minGeneIdentity,
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493 'coverage_depth', False, {})
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494 if args.reportSequenceCoverage:
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495 _ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
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496 data_by_gene, workdir, time_str, 'second_run',
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497 args.minGeneIdentity, 'sequence_coverage', False, {})
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498 else:
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499 print('Some sequences missing after ReMatCh module first run. Second run will not be'
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500 ' performed')
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501 if os.path.isfile(consensus_concatenated_fasta):
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502 os.remove(consensus_concatenated_fasta)
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503 if os.path.isdir(rematch_second_outdir):
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504 utils.remove_directory(rematch_second_outdir)
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505 else:
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506 print('No sequences left after ReMatCh module first run. Second run will not be performed')
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507 if os.path.isfile(consensus_concatenated_fasta):
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508 os.remove(consensus_concatenated_fasta)
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509 if os.path.isdir(rematch_second_outdir):
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510 utils.remove_directory(rematch_second_outdir)
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511
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512 if not searched_fastq_files and not args.keepDownloadedFastq and fastq_files is not None:
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513 for fastq in fastq_files:
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514 if os.path.isfile(fastq):
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515 os.remove(fastq)
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516
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517 time_taken = utils.run_time(sample_start_time)
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518
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519 write_sample_report(sample, workdir, time_str, file_size, run_successfully_fastq,
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520 run_successfully_rematch_first, run_successfully_rematch_second, time_taken_fastq,
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521 time_taken_rematch_first, time_taken_rematch_second, time_taken, sequencing_information,
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522 sample_data_general_first if run_successfully_rematch_first else
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523 {'number_absent_genes': None, 'number_genes_multiple_alleles': None,
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524 'mean_sample_coverage': None},
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525 sample_data_general_second if run_successfully_rematch_second else
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526 {'number_absent_genes': None, 'number_genes_multiple_alleles': None,
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527 'mean_sample_coverage': None},
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528 fastq_files if fastq_files is not None else '')
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529
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530 if all([run_successfully_fastq is not False,
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531 run_successfully_rematch_first is not False,
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532 run_successfully_rematch_second is not False]):
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533 number_samples_successfully += 1
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534
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535 if args.summary:
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536 write_summary_report(workdir, 'coverage_depth', time_str, gene_list_reference, genes_present_coverage_depth)
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537 if args.reportSequenceCoverage:
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538 write_summary_report(workdir, 'sequence_coverage', time_str, gene_list_reference,
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539 genes_present_sequence_coverage)
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540
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541 return number_samples_successfully, len(list_ids)
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542
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543
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544 def main():
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545 if sys.version_info[0] < 3:
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546 sys.exit('Must be using Python 3. Try calling "python3 rematch.py"')
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547
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548 parser = argparse.ArgumentParser(prog='rematch.py',
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549 description='Reads mapping against target sequences, checking mapping and'
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550 ' consensus sequences production',
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551 formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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552 parser.add_argument('--version', help='Version information', action='version',
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553 version='{prog} v{version}'.format(prog=parser.prog, version=__version__))
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554
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555 parser_optional_general = parser.add_argument_group('General facultative options')
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556 parser_optional_general.add_argument('-r', '--reference', type=argparse.FileType('r'),
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557 metavar='/path/to/reference_sequence.fasta',
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558 help='Fasta file containing reference sequences', required=False)
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559 parser_optional_general.add_argument('-w', '--workdir', type=str, metavar='/path/to/workdir/directory/',
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560 help='Path to the directory where ReMatCh will run and produce the outputs'
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561 ' with reads (ended with fastq.gz/fq.gz and, in case of PE data, pair-end'
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562 ' direction coded as _R1_001 / _R2_001 or _1 / _2) already'
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563 ' present (organized in sample folders) or to be downloaded',
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564 required=False, default='.')
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565 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use',
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566 required=False, default=1)
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567 parser_optional_general.add_argument('--mlst', type=str, metavar='"Streptococcus agalactiae"',
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568 help='Species name (same as in PubMLST) to be used in MLST'
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diff changeset
569 ' determination. ReMatCh will use Bowtie2 very-sensitive-local mapping'
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diff changeset
570 ' parameters and will recode the soft clip CIGAR flags of the first run',
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diff changeset
571 required=False)
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diff changeset
572 parser_optional_general.add_argument('--doNotUseProvidedSoftware', action='store_true',
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573 help='Tells ReMatCh to not use Bowtie2, Samtools and Bcftools that are'
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diff changeset
574 ' provided with it')
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parents:
diff changeset
575
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576 parser_optional_download_exclusive = parser.add_mutually_exclusive_group()
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577 parser_optional_download_exclusive.add_argument('-l', '--listIDs', type=argparse.FileType('r'),
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578 metavar='/path/to/list_IDs.txt',
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579 help='Path to list containing the IDs to be'
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580 ' downloaded (one per line)', required=False)
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581 parser_optional_download_exclusive.add_argument('-t', '--taxon', type=str, metavar='"Streptococcus agalactiae"',
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582 help='Taxon name for which ReMatCh will download fastq files',
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diff changeset
583 required=False)
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diff changeset
584
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585 parser_optional_rematch = parser.add_argument_group('ReMatCh module facultative options')
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586 parser_optional_rematch.add_argument('--extraSeq', type=int, metavar='N',
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587 help='Sequence length added to both ends of target sequences (usefull to'
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588 ' improve reads mapping to the target one) that will be trimmed in'
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589 ' ReMatCh outputs', required=False, default=0)
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590 parser_optional_rematch.add_argument('--minCovPresence', type=int, metavar='N',
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591 help='Reference position minimum coverage depth to consider the position to be'
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592 ' present in the sample', required=False, default=5)
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593 parser_optional_rematch.add_argument('--minCovCall', type=int, metavar='N',
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594 help='Reference position minimum coverage depth to perform a base call. Lower'
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595 ' coverage will be coded as N', required=False, default=10)
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596 parser_optional_rematch.add_argument('--minFrequencyDominantAllele', type=float, metavar='0.6',
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597 help='Minimum relative frequency of the dominant allele coverage depth (value'
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diff changeset
598 ' between [0, 1]). Positions with lower values will be considered as'
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599 ' having multiple alleles (and will be coded as N)', required=False,
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diff changeset
600 default=0.6)
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601 parser_optional_rematch.add_argument('--minGeneCoverage', type=int, metavar='N',
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602 help='Minimum percentage of target reference gene sequence covered'
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diff changeset
603 ' by --minCovPresence to consider a gene to be present (value'
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604 ' between [0, 100])', required=False, default=70)
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605 parser_optional_rematch.add_argument('--minGeneIdentity', type=int, metavar='N',
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606 help='Minimum percentage of identity of reference gene sequence covered'
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diff changeset
607 ' by --minCovCall to consider a gene to be present (value'
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diff changeset
608 ' between [0, 100]). One INDEL will be considered as one difference',
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609 required=False, default=80)
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610 parser_optional_rematch.add_argument('--numMapLoc', type=int, metavar='N', help=argparse.SUPPRESS, required=False,
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611 default=1)
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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)
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613 parser_optional_rematch.add_argument('--doubleRun', action='store_true',
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614 help='Tells ReMatCh to run a second time using as reference the noMatter'
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615 ' consensus sequence produced in the first run. This will improve'
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diff changeset
616 ' consensus sequence determination for sequences with high percentage of'
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diff changeset
617 ' target reference gene sequence covered')
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618 parser_optional_rematch.add_argument('--reportSequenceCoverage', action='store_true',
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619 help='Produce an extra combined_report.data_by_gene with the sequence coverage'
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diff changeset
620 ' instead of coverage depth')
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621 parser_optional_rematch.add_argument('--summary', action='store_true',
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622 help='Produce extra report files containing only sequences present in at least'
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diff changeset
623 ' one sample (usefull when using a large number of reference'
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diff changeset
624 ' sequences, and only for first run)')
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625 parser_optional_rematch.add_argument('--notWriteConsensus', action='store_true',
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626 help='Do not write consensus sequences')
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627 parser_optional_rematch.add_argument('--bowtieAlgo', type=str, metavar='"--very-sensitive-local"',
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628 help='Bowtie2 alignment mode. It can be an end-to-end alignment (unclipped'
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diff changeset
629 ' alignment) or local alignment (soft clipped alignment). Also, can'
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diff changeset
630 ' choose between fast or sensitive alignments. Please check Bowtie2'
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diff changeset
631 ' manual for extra'
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diff changeset
632 ' information: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml .'
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diff changeset
633 ' This option should be provided between quotes and starting with'
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diff changeset
634 ' an empty space (like --bowtieAlgo " --very-fast") or using equal'
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635 ' sign (like --bowtieAlgo="--very-fast")',
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636 required=False, default='--very-sensitive-local')
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637 parser_optional_rematch.add_argument('--bowtieOPT', type=str, metavar='"--no-mixed"',
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638 help='Extra Bowtie2 options. This option should be provided between quotes and'
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diff changeset
639 ' starting with an empty space (like --bowtieOPT " --no-mixed") or using'
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diff changeset
640 ' equal sign (like --bowtieOPT="--no-mixed")',
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641 required=False)
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642 parser_optional_rematch.add_argument('--debug', action='store_true',
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643 help='DeBug Mode: do not remove temporary files')
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644
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645 parser_optional_mlst = parser.add_argument_group('MLST facultative options')
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646 parser_optional_rematch.add_argument('--mlstReference', action='store_true',
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647 help='If the curated scheme for MLST alleles is available, tells ReMatCh to'
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diff changeset
648 ' use these as reference (force Bowtie2 to run with very-sensitive-local'
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diff changeset
649 ' parameters, and sets --extraSeq to 200), otherwise ReMatCh uses the'
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diff changeset
650 ' first alleles of each MLST gene fragment in PubMLST as reference'
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diff changeset
651 ' sequences (force Bowtie2 to run with very-sensitive-local parameters,'
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diff changeset
652 ' and sets --extraSeq to 0)')
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653 parser_optional_mlst.add_argument('--mlstSchemaNumber', type=int, metavar='N',
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654 help='Number of the species PubMLST schema to be used in case of multiple schemes'
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655 ' available (by default will use the first schema)', required=False)
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656 parser_optional_mlst.add_argument('--mlstConsensus', choices=['noMatter', 'correct', 'alignment', 'all'], type=str,
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657 metavar='noMatter',
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658 help='Consensus sequence to be used in MLST'
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659 ' determination (available options: %(choices)s)', required=False,
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660 default='noMatter')
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661 parser_optional_mlst.add_argument('--mlstRun', choices=['first', 'second', 'all'], type=str, metavar='first',
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662 help='ReMatCh run outputs to be used in MLST determination (available'
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663 ' options: %(choices)s)', required=False, default='all')
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664
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665 parser_optional_download = parser.add_argument_group('Download facultative options')
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666 parser_optional_download.add_argument('-a', '--asperaKey', type=argparse.FileType('r'),
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667 metavar='/path/to/asperaweb_id_dsa.openssh',
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668 help='Tells ReMatCh to download fastq files from ENA using Aspera'
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669 ' Connect. With this option, the path to Private-key file'
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670 ' asperaweb_id_dsa.openssh must be provided (normaly found in'
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671 ' ~/.aspera/connect/etc/asperaweb_id_dsa.openssh).', required=False)
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672 parser_optional_download.add_argument('-k', '--keepDownloadedFastq', action='store_true',
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673 help='Tells ReMatCh to keep the fastq files downloaded')
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674 parser_optional_download.add_argument('--downloadLibrariesType', type=str, metavar='PAIRED',
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675 help='Tells ReMatCh to download files with specific library'
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676 ' layout (available options: %(choices)s)',
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677 choices=['PAIRED', 'SINGLE', 'BOTH'], required=False, default='BOTH')
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678 parser_optional_download.add_argument('--downloadInstrumentPlatform', type=str, metavar='ILLUMINA',
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679 help='Tells ReMatCh to download files with specific library layout (available'
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680 ' options: %(choices)s)', choices=['ILLUMINA', 'ALL'], required=False,
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681 default='ILLUMINA')
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682 parser_optional_download.add_argument('--downloadCramBam', action='store_true',
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683 help='Tells ReMatCh to also download cram/bam files and convert them to fastq'
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684 ' files')
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685
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686 parser_optional_sra = parser.add_mutually_exclusive_group()
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687 parser_optional_sra.add_argument('--SRA', action='store_true',
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688 help='Tells getSeqENA.py to download reads in fastq format only from NCBI SRA'
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689 ' database (not recommended)')
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690 parser_optional_sra.add_argument('--SRAopt', action='store_true',
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691 help='Tells getSeqENA.py to download reads from NCBI SRA if the download from ENA'
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692 ' fails')
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693
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694 parser_optional_soft_clip = parser.add_argument_group('Soft clip facultative options')
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695 parser_optional_soft_clip.add_argument('--softClip_baseQuality', type=int, metavar='N',
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696 help='Base quality phred score in reads soft clipped regions',
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697 required=False,
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698 default=7)
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699 parser_optional_soft_clip.add_argument('--softClip_recodeRun', type=str, metavar='first',
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700 help='ReMatCh run to recode soft clipped regions (available'
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701 ' options: %(choices)s)', choices=['first', 'second', 'both', 'none'],
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702 required=False, default='none')
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703 parser_optional_soft_clip.add_argument('--softClip_cigarFlagRecode', type=str, metavar='M',
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704 help='CIGAR flag to recode CIGAR soft clip (available options: %(choices)s)',
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705 choices=['M', 'I', 'X'], required=False, default='X')
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706
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707 args = parser.parse_args()
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708
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709 msg = []
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710 if args.reference is None and not args.mlstReference:
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711 msg.append('At least --reference or --mlstReference should be provided')
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712 elif args.reference is not None and args.mlstReference:
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713 msg.append('Only --reference or --mlstReference should be provided')
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714 else:
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715 if args.mlstReference:
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716 if args.mlst is None:
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717 msg.append('Please provide species name using --mlst')
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718 if args.minFrequencyDominantAllele < 0 or args.minFrequencyDominantAllele > 1:
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719 msg.append('--minFrequencyDominantAllele should be a value between [0, 1]')
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720 if args.minGeneCoverage < 0 or args.minGeneCoverage > 100:
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721 msg.append('--minGeneCoverage should be a value between [0, 100]')
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722 if args.minGeneIdentity < 0 or args.minGeneIdentity > 100:
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723 msg.append('--minGeneIdentity should be a value between [0, 100]')
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724 if args.notWriteConsensus and args.doubleRun:
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725 msg.append('--notWriteConsensus and --doubleRun cannot be used together.'
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726 ' Maybe you only want to use --doubleRun')
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727
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728 if len(msg) > 0:
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729 argparse.ArgumentParser.error('\n'.join(msg))
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730
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731 start_time = time.time()
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732
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733 number_samples_successfully, samples_total_number = run_rematch(args)
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734
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735 print('\n' + 'END ReMatCh')
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736 print('\n' +
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737 str(number_samples_successfully) + ' samples out of ' + str(samples_total_number) + ' run successfully')
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738 time_taken = utils.run_time(start_time)
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739 del time_taken
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740
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741 if number_samples_successfully == 0:
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742 sys.exit('No samples run successfully!')
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743
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744
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745 if __name__ == "__main__":
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746 main()