Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/patho_typing.py @ 0:965517909457 draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 08:41:44 -0500
parents
children 0cbed1c0a762
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1 #!/usr/bin/env python
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2
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3 # -*- coding: utf-8 -*-
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4
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5 """
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6 patho_typing.py - In silico pathogenic typing directly from raw
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7 Illumina reads
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8 <https://github.com/B-UMMI/patho_typing/>
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9
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10 Copyright (C) 2017 Miguel Machado <mpmachado@medicina.ulisboa.pt>
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11
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12 Last modified: July 06, 2017
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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 2017-12-05 ISS
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28 In order to use the module within the EURL_WGS_Typer pipeline with a
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29 different virulence database for E coli, mapping against the
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30 typing_rules.tab was deactivated.
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31 """
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32
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33 import argparse
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34 import os
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35 import time
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36 import sys
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37
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38 import modules.utils as utils
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39 import modules.run_rematch as run_rematch
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40 import modules.typing as typing
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41
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42 version = '0.3'
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43
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44
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45 def set_reference(species, outdir, script_path, trueCoverage):
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46 reference_file = None
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47 trueCoverage_file = None
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48 trueCoverage_sequences = None
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49 trueCoverage_headers = None
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50 trueCoverage_config = None
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51 typing_file = None
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52 typing_sequences = None
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53 typing_headers = None
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54 typing_rules = None
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55 typing_config = None
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56
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57 species_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf', '_'.join([s.lower() for s in species]), '')
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58
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59 if os.path.isdir(species_folder):
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60 typing_rules = os.path.join(species_folder, 'typing_rules.tab')
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61 typing_file = os.path.join(species_folder, 'typing.fasta')
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62 typing_sequences, ignore = utils.get_sequence_information(typing_file, 0)
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63 typing_sequences, typing_headers = utils.clean_headers_sequences(typing_sequences)
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64 typing_sequences = utils.simplify_sequence_dict(typing_sequences)
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65 typing_config = os.path.join(species_folder, 'typing.config')
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66 if trueCoverage:
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67 trueCoverage_file = os.path.join(species_folder, 'trueCoverage.fasta')
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68 trueCoverage_sequences, ignore = utils.get_sequence_information(trueCoverage_file, 0)
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69 trueCoverage_sequences, trueCoverage_headers = utils.clean_headers_sequences(trueCoverage_sequences)
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70 trueCoverage_sequences = utils.simplify_sequence_dict(trueCoverage_sequences)
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71 trueCoverage_config = os.path.join(species_folder, 'trueCoverage.config')
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72
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73 trueCoverage_typing_sequences = trueCoverage_sequences.copy()
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74 for header in typing_sequences:
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75 if header not in trueCoverage_sequences:
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76 trueCoverage_typing_sequences[header] = typing_sequences[header]
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77 else:
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78 print 'Sequence {header} of typing.fasta already present in trueCoverage.fasta'.format(header=header)
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79
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80 reference_file = os.path.join(outdir, 'trueCoverage_typing.fasta')
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81 write_sequeces(reference_file, trueCoverage_typing_sequences)
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82 else:
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83 reference_file = os.path.join(outdir, 'typing.fasta')
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84 write_sequeces(reference_file, typing_sequences)
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85 else:
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86 species_present = []
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87 seq_conf_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf', '')
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88 species_folder = [d for d in os.listdir(seq_conf_folder) if not d.startswith('.') and os.path.isdir(os.path.join(seq_conf_folder, d, ''))]
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89 for species in species_folder:
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90 species = species.split('_')
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91 species[0] = species[0][0].upper() + species[0][1:]
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92 species_present.append(' '.join(species))
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93 sys.exit('Only these species are available:' + '\n' + '\n'.join(species_present))
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94
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95 return reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, typing_file, typing_sequences, typing_headers, typing_rules, typing_config
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96
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97
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98 def confirm_genes_fasta_rules(typing_fasta_headers, typing_rules_file):
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99 with open(typing_rules_file, 'rtU') as reader:
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100 genes = []
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101 for line in reader:
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102 line = line.splitlines()[0]
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103 if len(line) > 0:
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104 line = line.split('\t')
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105 if line[0].startswith('#'):
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106 genes = line[1:]
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107 break
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108 missing_genes = []
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109 for gene in genes:
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110 if gene.lower() not in typing_fasta_headers:
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111 missing_genes.append(gene)
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112 if len(missing_genes) > 0:
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113 sys.exit('The following genes required for typing are not present in typing fasta file: {missing_genes}'.format(missing_genes=', '.join(missing_genes)))
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114
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115
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116 def index_fasta_samtools(fasta, region_None, region_outfile_none, print_comand_True):
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117 command = ['samtools', 'faidx', fasta, '', '', '']
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118 shell_true = False
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119 if region_None is not None:
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120 command[3] = region_None
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121 if region_outfile_none is not None:
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122 command[4] = '>'
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123 command[5] = region_outfile_none
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124 shell_true = True
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125 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, shell_true, None, print_comand_True)
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126 return run_successfully, stdout
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127
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128
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129 def indexSequenceBowtie2(referenceFile, threads):
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130 if os.path.isfile(str(referenceFile + '.1.bt2')):
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131 run_successfully = True
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132 else:
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133 command = ['bowtie2-build', '--threads', str(threads), referenceFile, referenceFile]
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134 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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135 return run_successfully
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136
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137
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138 def run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
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139 sam_file = os.path.join(outdir, str('alignment.sam'))
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140
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141 run_successfully = indexSequenceBowtie2(referenceFile, threads)
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142 if run_successfully:
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143 command = ['bowtie2', '-k', str(numMapLoc), '-q', '', '--threads', str(threads), '-x', referenceFile, '', '--no-unal', '-S', sam_file]
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144
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145 if len(fastq_files) == 1:
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146 command[9] = '-U ' + fastq_files[0]
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147 elif len(fastq_files) == 2:
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148 command[9] = '-1 ' + fastq_files[0] + ' -2 ' + fastq_files[1]
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149 else:
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150 return False, None
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151
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152 if conserved_True:
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153 command[4] = '--sensitive'
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154 else:
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155 command[4] = '--very-sensitive-local'
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156
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157 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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158
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159 if not run_successfully:
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160 sam_file = None
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161
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162 return run_successfully, sam_file
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163
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164
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165 def sortAlignment(alignment_file, output_file, sortByName_True, threads):
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166 outFormat_string = os.path.splitext(output_file)[1][1:].lower()
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167 command = ['samtools', 'sort', '-o', output_file, '-O', outFormat_string, '', '-@', str(threads), alignment_file]
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168 if sortByName_True:
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169 command[6] = '-n'
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170 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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171 if not run_successfully:
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172 output_file = None
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173 return run_successfully, output_file
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174
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175
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176 def indexAlignment(alignment_file):
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177 command = ['samtools', 'index', alignment_file]
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178 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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179 return run_successfully
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180
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181
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182 def mapping_reads(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
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183 print '\n' + 'Mapping the reads' + '\n'
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184 run_successfully, sam_file = run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc)
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185 if run_successfully:
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186 run_successfully, bam_file = sortAlignment(sam_file, str(os.path.splitext(sam_file)[0] + '.bam'), False, threads)
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187 if run_successfully:
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188 os.remove(sam_file)
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189 run_successfully = indexAlignment(bam_file)
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190 if run_successfully:
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191 index_fasta_samtools(referenceFile, None, None, True)
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192 return run_successfully, bam_file
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193
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194
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195 def include_rematch_dependencies_path():
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196 command = ['which', 'rematch.py']
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197 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, False)
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198 if run_successfully:
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199 rematch = stdout.splitlines()[0]
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200 utils.setPATHvariable(False, rematch)
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201 return rematch
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202
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203
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204 def split_bam(bam_file, list_sequences, outdir, threads):
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205 new_bam = os.path.join(outdir, 'partial.bam')
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206 command = ['samtools', 'view', '-b', '-u', '-h', '-o', new_bam, '-@', str(threads), bam_file, ' '.join(list_sequences)]
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207 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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208 return run_successfully, new_bam
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209
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210
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211 def parse_config(config_file):
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212 config = {'reference_file': None, 'length_extra_seq': None, 'maximum_number_absent_genes': None, 'maximum_number_genes_multiple_alleles': None, 'minimum_read_coverage': None, 'minimum_depth_presence': None, 'minimum_depth_call': None, 'minimum_depth_frequency_dominant_allele': None, 'minimum_gene_coverage': None, 'minimum_gene_identity': None}
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213
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214 with open(config_file, 'rtU') as reader:
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215 field = None
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216 for line in reader:
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217 line = line.splitlines()[0]
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218 if len(line) > 0:
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219 line = line.split(' ')[0]
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220 if line.startswith('#'):
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221 line = line[1:].split(' ')[0]
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222 field = line
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223 else:
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224 if field is not None:
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225 if field in ['length_extra_seq', 'maximum_number_absent_genes', 'maximum_number_genes_multiple_alleles', 'minimum_read_coverage', 'minimum_depth_presence', 'minimum_depth_call', 'minimum_gene_coverage', 'minimum_gene_identity']:
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226 line = int(line)
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227 if field in ['minimum_gene_coverage', 'minimum_gene_identity']:
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228 if line < 0 or line > 100:
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229 sys.exit('minimum_gene_coverage in trueCoverage_rematch config file must be an integer between 0 and 100')
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230 elif field == 'minimum_depth_frequency_dominant_allele':
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231 line = float(line)
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232 if line < 0 or line > 1:
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233 sys.exit('minimum_depth_frequency_dominant_allele in trueCoverage_rematch config file must be a double between 0 and 1')
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234 config[field] = line
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235 field = None
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236
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237 for field in config:
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238 if config[field] is None:
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239 sys.exit(field + ' in trueCoverage_rematch config file is missing')
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240
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241 return config
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242
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243
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244 def clean_pathotyping_folder(outdir, reference_file, debug_mode_true):
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245 if not debug_mode_true:
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246 files = [f for f in os.listdir(outdir) if not f.startswith('.') and os.path.isfile(os.path.join(outdir, f))]
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247 for file_found in files:
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248 if file_found.startswith(('alignment.', os.path.splitext(os.path.basename(reference_file))[0])):
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249 file_found = os.path.join(outdir, file_found)
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250 os.remove(file_found)
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251
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252
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253 def write_sequeces(out_file, sequences_dict):
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254 with open(out_file, 'wt') as writer:
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255 for header in sequences_dict:
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256 writer.write('>' + header + '\n')
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257 writer.write('\n'.join(utils.chunkstring(sequences_dict[header]['sequence'], 80)) + '\n')
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258
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259
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260 def main():
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261 parser = argparse.ArgumentParser(prog='patho_typing.py', description='In silico pathogenic typing directly from raw Illumina reads', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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262 parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
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263
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264 parser_required = parser.add_argument_group('Required options')
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265 parser_required.add_argument('-f', '--fastq', nargs='+', action=utils.required_length((1, 2), '--fastq'), type=argparse.FileType('r'), metavar=('/path/to/input/file.fq.gz'), help='Path to single OR paired-end fastq files. If two files are passed, they will be assumed as being the paired fastq files', required=True)
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266 parser_required.add_argument('-s', '--species', nargs=2, type=str, metavar=('Yersinia', 'enterocolitica'), help='Species name', required=True)
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267
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268 parser_optional_general = parser.add_argument_group('General facultative options')
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269 parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/path/to/output/directory/', help='Path to the directory where the information will be stored', required=False, default='.')
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270 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use', required=False, default=1)
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271 parser_optional_general.add_argument('--trueCoverage', action='store_true', help='Assess true coverage before continue typing')
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272 parser_optional_general.add_argument('--noCheckPoint', action='store_true', help='Ignore the true coverage checking point')
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273 parser_optional_general.add_argument('--minGeneCoverage', type=int, metavar='N', help='Minimum typing percentage of target reference gene sequence covered to consider a gene to be present (value between [0, 100])', required=False)
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274 parser_optional_general.add_argument('--minGeneIdentity', type=int, metavar='N', help='Minimum typing percentage of identity of reference gene sequence covered to consider a gene to be present (value between [0, 100]). One INDEL will be considered as one difference', required=False)
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275 parser_optional_general.add_argument('--minGeneDepth', type=int, metavar='N', help='Minimum typing gene average coverage depth of present positions to consider a gene to be present (default 15, or 1/3 of average sample coverage assessed by true coverage analysis)', required=False)
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276 parser_optional_general.add_argument('--doNotRemoveConsensus', action='store_true', help='Do not remove ReMatCh consensus sequences')
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277 parser_optional_general.add_argument('--debug', action='store_true', help='DeBug Mode: do not remove temporary files')
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278
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279 args = parser.parse_args()
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280
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281 if args.minGeneCoverage is not None and (args.minGeneCoverage < 0 or args.minGeneCoverage > 100):
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282 parser.error('--minGeneCoverage should be a value between [0, 100]')
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283 if args.minGeneIdentity is not None and (args.minGeneIdentity < 0 or args.minGeneIdentity > 100):
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284 parser.error('--minGeneIdentity should be a value between [0, 100]')
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285
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286 start_time = time.time()
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287
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288 args.outdir = os.path.abspath(args.outdir)
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289 if not os.path.isdir(args.outdir):
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290 os.makedirs(args.outdir)
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291
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292 # Start logger
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293 logfile, time_str = utils.start_logger(args.outdir)
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294
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295 script_path = utils.general_information(logfile, version, args.outdir, time_str)
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296 print '\n'
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297
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298 rematch = include_rematch_dependencies_path()
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299
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300 args.fastq = [fastq.name for fastq in args.fastq]
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301
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302 reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, typing_file, typing_sequences, typing_headers, typing_rules, typing_config = set_reference(args.species, args.outdir, script_path, args.trueCoverage)
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303 original_reference_file = str(reference_file)
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304
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305 #confirm_genes_fasta_rules(typing_headers, typing_rules)
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306
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307 run_successfully, bam_file = mapping_reads(args.fastq, reference_file, args.threads, args.outdir, False, 1)
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308 if run_successfully:
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309 rematch_dir = os.path.join(args.outdir, 'rematch', '')
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310 if not os.path.isdir(rematch_dir):
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311 os.makedirs(rematch_dir)
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312
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313 if args.trueCoverage:
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314 trueCoverage_dir = os.path.join(rematch_dir, 'trueCoverage', '')
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315 if not os.path.isdir(trueCoverage_dir):
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316 os.makedirs(trueCoverage_dir)
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317
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318 print '\n'
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319 run_successfully, trueCoverage_bam = split_bam(bam_file, trueCoverage_headers, trueCoverage_dir, args.threads)
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320 if run_successfully:
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321 run_successfully = indexAlignment(trueCoverage_bam)
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322 if run_successfully:
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323 reference_file = os.path.join(trueCoverage_dir, 'reference.fasta')
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324 write_sequeces(reference_file, trueCoverage_sequences)
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325 index_fasta_samtools(reference_file, None, None, True)
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326 config = parse_config(trueCoverage_config)
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327 runtime, run_successfully, sample_data_general, data_by_gene = run_rematch.run_rematch(rematch, trueCoverage_dir, reference_file, trueCoverage_bam, args.threads, config['length_extra_seq'], config['minimum_depth_presence'], config['minimum_depth_call'], config['minimum_depth_frequency_dominant_allele'], config['minimum_gene_coverage'], config['minimum_gene_identity'], args.debug, args.doNotRemoveConsensus)
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328
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329 if run_successfully and sample_data_general['mean_sample_coverage'] is not None and sample_data_general['number_absent_genes'] is not None and sample_data_general['number_genes_multiple_alleles'] is not None:
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330 if args.minGeneDepth is None:
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331 args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3
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332
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333 exit_info = []
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334 if sample_data_general['mean_sample_coverage'] < config['minimum_read_coverage']:
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335 exit_info.append('Sample coverage ({mean_sample_coverage}) lower than the minimum required ({minimum_read_coverage})'.format(mean_sample_coverage=sample_data_general['mean_sample_coverage'], minimum_read_coverage=config['minimum_read_coverage']))
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336 if sample_data_general['number_absent_genes'] > config['maximum_number_absent_genes']:
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337 exit_info.append('Number of absent genes ({number_absent_genes}) higher than the maximum allowed ({maximum_number_absent_genes})'.format(number_absent_genes=sample_data_general['number_absent_genes'], maximum_number_absent_genes=config['maximum_number_absent_genes']))
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338 if sample_data_general['number_genes_multiple_alleles'] > config['maximum_number_genes_multiple_alleles']:
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339 exit_info.append('Number of genes with multiple alleles ({number_genes_multiple_alleles}) higher than the maximum allowed ({maximum_number_genes_multiple_alleles})'.format(number_genes_multiple_alleles=sample_data_general['number_genes_multiple_alleles'], maximum_number_genes_multiple_alleles=config['maximum_number_genes_multiple_alleles']))
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340
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341 if len(exit_info) > 0:
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342 print '\n' + '\n'.join(exit_info) + '\n'
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343 e = 'TrueCoverage requirements not fulfilled'
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344 print '\n' + e + '\n'
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345 if not args.noCheckPoint:
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346 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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347 time_taken = utils.runTime(start_time)
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348 sys.exit(e)
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349 else:
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350 e = 'TrueCoverage module did not run successfully'
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351 print '\n' + e + '\n'
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352 if not args.noCheckPoint:
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353 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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354 time_taken = utils.runTime(start_time)
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355 sys.exit(e)
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356
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357 print '\n'
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358 typing_dir = os.path.join(rematch_dir, 'typing', '')
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359 if not os.path.isdir(typing_dir):
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360 os.makedirs(typing_dir)
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361 run_successfully, bam_file = split_bam(bam_file, typing_headers, typing_dir, args.threads)
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362 if run_successfully:
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363 run_successfully = indexAlignment(bam_file)
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364 if run_successfully:
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365 reference_file = os.path.join(typing_dir, 'reference.fasta')
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366 write_sequeces(reference_file, typing_sequences)
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367 index_fasta_samtools(reference_file, None, None, True)
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368 rematch_dir = str(typing_dir)
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369 if not run_successfully:
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370 if args.noCheckPoint:
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371 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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372 time_taken = utils.runTime(start_time)
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373 sys.exit('Something in the required TrueCoverage analysis went wrong')
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374
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375 if run_successfully:
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376 config = parse_config(typing_config)
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377 if args.minGeneCoverage is not None:
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378 config['minimum_gene_coverage'] = args.minGeneCoverage
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379 if args.minGeneIdentity is not None:
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380 config['minimum_gene_identity'] = args.minGeneIdentity
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381
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382 runtime, run_successfully, sample_data_general, data_by_gene = run_rematch.run_rematch(rematch, rematch_dir, reference_file, bam_file, args.threads, config['length_extra_seq'], config['minimum_depth_presence'], config['minimum_depth_call'], config['minimum_depth_frequency_dominant_allele'], config['minimum_gene_coverage'], config['minimum_gene_identity'], args.debug, args.doNotRemoveConsensus)
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383 if run_successfully and data_by_gene is not None:
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384 if args.minGeneDepth is None:
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385 args.minGeneDepth = 15
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386
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387 #runtime, ignore, ignore = typing.typing(data_by_gene, typing_rules, config['minimum_gene_coverage'], config['minimum_gene_identity'], args.minGeneDepth, args.outdir)
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388 else:
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389 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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390 time_taken = utils.runTime(start_time)
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391 sys.exit('ReMatCh run for pathotyping did not run successfully')
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392 else:
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393 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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394 time_taken = utils.runTime(start_time)
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395 sys.exit('Something did not run successfully')
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396
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397 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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398
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399 print '\n'
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400 time_taken = utils.runTime(start_time)
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401 del time_taken
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402
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403
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404 if __name__ == "__main__":
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405 main()