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annotate scripts/patho_typing.py @ 3:0cbed1c0a762 draft default tip

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
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3
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1 #!/usr/bin/env python3
0
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2
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3 # -*- coding: utf-8 -*-
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4
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5 """
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6 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
3
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10 Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
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11
3
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12 Last modified: October 15, 2018
0
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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
3
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27 2020-01-13 ISS
0
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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
3
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37 from pkg_resources import resource_filename
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38
3
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39 try:
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40 from __init__ import __version__
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41
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42 import modules.utils as utils
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43 import modules.run_rematch as run_rematch
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44 import modules.typing as typing
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45 except ImportError:
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46 from pathotyping.__init__ import __version__
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47
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48 from pathotyping.modules import utils as utils
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49 from pathotyping.modules import run_rematch as run_rematch
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50 from pathotyping.modules import typing as typing
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51
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52
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53 def set_reference(species, outdir, script_path, trueCoverage):
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54 reference_file = None
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55 trueCoverage_file = None
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56 trueCoverage_sequences = None
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57 trueCoverage_headers = None
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58 trueCoverage_config = None
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59 typing_file = None
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60 typing_sequences = None
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61 typing_headers = None
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62 typing_rules = None
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63 typing_config = None
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64
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65 species_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf',
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66 '_'.join([s.lower() for s in species]), '')
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67
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68 if os.path.isdir(species_folder):
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69 typing_rules = os.path.join(species_folder, 'typing_rules.tab')
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70 typing_file = os.path.join(species_folder, 'typing.fasta')
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71 typing_sequences, ignore = utils.get_sequence_information(typing_file, 0)
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72 typing_sequences, typing_headers = utils.clean_headers_sequences(typing_sequences)
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73 typing_sequences = utils.simplify_sequence_dict(typing_sequences)
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74 typing_config = os.path.join(species_folder, 'typing.config')
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75 if trueCoverage:
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76 if os.path.isfile(os.path.join(species_folder, 'trueCoverage.fasta')):
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77 trueCoverage_file = os.path.join(species_folder, 'trueCoverage.fasta')
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78 trueCoverage_sequences, ignore = utils.get_sequence_information(trueCoverage_file, 0)
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79 trueCoverage_sequences, trueCoverage_headers = utils.clean_headers_sequences(trueCoverage_sequences)
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80 trueCoverage_sequences = utils.simplify_sequence_dict(trueCoverage_sequences)
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81 trueCoverage_config = os.path.join(species_folder, 'trueCoverage.config')
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82
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83 trueCoverage_typing_sequences = trueCoverage_sequences.copy()
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84 for header in typing_sequences:
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85 if header not in trueCoverage_sequences:
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86 trueCoverage_typing_sequences[header] = typing_sequences[header]
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87 else:
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88 print('Sequence {header} of typing.fasta already present in'
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89 ' trueCoverage.fasta'.format(header=header))
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90
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91 reference_file = os.path.join(outdir, 'trueCoverage_typing.fasta')
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92 write_sequeces(reference_file, trueCoverage_typing_sequences)
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93 else:
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94 reference_file = os.path.join(outdir, 'typing.fasta')
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95 write_sequeces(reference_file, typing_sequences)
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96 else:
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97 species_present = []
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98 seq_conf_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf', '')
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99 species_folder = [d for d in os.listdir(seq_conf_folder) if
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100 not d.startswith('.') and os.path.isdir(os.path.join(seq_conf_folder, d, ''))]
0
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101 for species in species_folder:
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102 species = species.split('_')
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103 species[0] = species[0][0].upper() + species[0][1:]
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104 species_present.append(' '.join(species))
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105 sys.exit('Only these species are available:' + '\n' + '\n'.join(species_present))
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106
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107 return reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, \
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108 typing_file, typing_sequences, typing_headers, typing_rules, typing_config
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109
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110
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111 def index_fasta_samtools(fasta, region_None, region_outfile_none, print_comand_True):
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112 command = ['samtools', 'faidx', fasta, '', '', '']
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113 shell_true = False
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114 if region_None is not None:
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115 command[3] = region_None
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116 if region_outfile_none is not None:
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117 command[4] = '>'
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118 command[5] = region_outfile_none
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119 shell_true = True
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120 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, shell_true, None, print_comand_True)
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121 return run_successfully, stdout
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122
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123
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124 def indexSequenceBowtie2(referenceFile, threads):
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125 if os.path.isfile(str(referenceFile + '.1.bt2')):
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126 run_successfully = True
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127 else:
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128 command = ['bowtie2-build', '--threads', str(threads), referenceFile, referenceFile]
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129 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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130 return run_successfully
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131
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132
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133 def run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
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134 sam_file = os.path.join(outdir, str('alignment.sam'))
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135
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136 run_successfully = indexSequenceBowtie2(referenceFile, threads)
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137 if run_successfully:
3
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138 command = ['bowtie2', '-k', str(numMapLoc), '-q', '', '--threads', str(threads), '-x', referenceFile, '',
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139 '--no-unal', '-S', sam_file]
0
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140
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141 if len(fastq_files) == 1:
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142 command[9] = '-U ' + fastq_files[0]
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143 elif len(fastq_files) == 2:
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144 command[9] = '-1 ' + fastq_files[0] + ' -2 ' + fastq_files[1]
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145 else:
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146 return False, None
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147
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148 if conserved_True:
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149 command[4] = '--sensitive'
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150 else:
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151 command[4] = '--very-sensitive-local'
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152
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153 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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154
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155 if not run_successfully:
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156 sam_file = None
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157
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158 return run_successfully, sam_file
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159
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160
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161 def sortAlignment(alignment_file, output_file, sortByName_True, threads):
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162 outFormat_string = os.path.splitext(output_file)[1][1:].lower()
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163 command = ['samtools', 'sort', '-o', output_file, '-O', outFormat_string, '', '-@', str(threads), alignment_file]
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164 if sortByName_True:
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165 command[6] = '-n'
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166 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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167 if not run_successfully:
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168 output_file = None
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169 return run_successfully, output_file
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170
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171
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172 def indexAlignment(alignment_file):
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173 command = ['samtools', 'index', alignment_file]
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174 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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175 return run_successfully
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176
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177
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178 def mapping_reads(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
3
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179 print('\n' + 'Mapping the reads' + '\n')
0
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180 run_successfully, sam_file = run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc)
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181 bam_file = None
0
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182 if run_successfully:
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183 run_successfully, bam_file = sortAlignment(sam_file, str(os.path.splitext(sam_file)[0] + '.bam'), False,
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184 threads)
0
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185 if run_successfully:
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186 os.remove(sam_file)
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187 run_successfully = indexAlignment(bam_file)
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188 if run_successfully:
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189 index_fasta_samtools(referenceFile, None, None, True)
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190 return run_successfully, bam_file
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191
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192
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193 def include_rematch_dependencies_path():
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194 original_rematch = None
0
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195 command = ['which', 'rematch.py']
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196 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, False)
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197 if run_successfully:
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198 original_rematch = stdout.splitlines()[0]
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199
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200 resource_rematch = None
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201 try:
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202 resource_rematch = resource_filename('ReMatCh', 'rematch.py')
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203 except ModuleNotFoundError:
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204 resource_rematch = original_rematch
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205 else:
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206 print('\n'
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207 'Using ReMatCh "{resource_rematch}" via "{original_rematch}"\n'.format(resource_rematch=resource_rematch,
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208 original_rematch=original_rematch))
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209
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210 if resource_rematch is not None:
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211 utils.setPATHvariable(False, resource_rematch)
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212 else:
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213 sys.exit('ReMatCh not found in the PATH')
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214
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215 return resource_rematch
0
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216
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217
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218 def split_bam(bam_file, list_sequences, outdir, threads):
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219 new_bam = os.path.join(outdir, 'partial.bam')
3
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220 command = ['samtools', 'view', '-b', '-u', '-h', '-o', new_bam, '-@', str(threads), bam_file,
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221 ' '.join(list_sequences)]
0
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222 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
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223 return run_successfully, new_bam
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224
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225
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226 def parse_config(config_file):
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227 config = {'reference_file': None, 'length_extra_seq': None, 'maximum_number_absent_genes': None,
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228 'maximum_number_genes_multiple_alleles': None, 'minimum_read_coverage': None,
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229 'minimum_depth_presence': None, 'minimum_depth_call': None,
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230 'minimum_depth_frequency_dominant_allele': None, 'minimum_gene_coverage': None,
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231 'minimum_gene_identity': None}
0
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232
3
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233 with open(config_file, 'rt') as reader:
0
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234 field = None
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235 for line in reader:
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236 line = line.splitlines()[0]
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237 if len(line) > 0:
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238 line = line.split(' ')[0]
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239 if line.startswith('#'):
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240 line = line[1:].split(' ')[0]
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241 field = line
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242 else:
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243 if field is not None:
3
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244 if field in ['length_extra_seq', 'maximum_number_absent_genes',
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245 'maximum_number_genes_multiple_alleles', 'minimum_read_coverage',
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246 'minimum_depth_presence', 'minimum_depth_call', 'minimum_gene_coverage',
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247 'minimum_gene_identity']:
0
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248 line = int(line)
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249 if field in ['minimum_gene_coverage', 'minimum_gene_identity']:
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250 if line < 0 or line > 100:
3
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251 sys.exit('minimum_gene_coverage in trueCoverage_rematch config file must be an'
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252 ' integer between 0 and 100')
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253 elif field == 'minimum_depth_frequency_dominant_allele':
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254 line = float(line)
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255 if line < 0 or line > 1:
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256 sys.exit('minimum_depth_frequency_dominant_allele in trueCoverage_rematch config file'
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257 ' must be a double between 0 and 1')
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258 config[field] = line
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259 field = None
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260
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261 for field in config:
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262 if config[field] is None:
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263 sys.exit(field + ' in trueCoverage_rematch config file is missing')
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264
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265 return config
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266
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267
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268 def clean_pathotyping_folder(outdir, reference_file, debug_mode_true):
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269 if not debug_mode_true:
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270 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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271 for file_found in files:
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272 if file_found.startswith(('alignment.', os.path.splitext(os.path.basename(reference_file))[0])):
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273 file_found = os.path.join(outdir, file_found)
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274 os.remove(file_found)
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275
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276
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277 def write_sequeces(out_file, sequences_dict):
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278 with open(out_file, 'wt') as writer:
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279 for header in sequences_dict:
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280 writer.write('>' + header + '\n')
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281 writer.write('\n'.join(utils.chunkstring(sequences_dict[header]['sequence'], 80)) + '\n')
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282
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283
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284 def main():
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285 parser = argparse.ArgumentParser(prog='patho_typing.py',
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286 description='In silico pathogenic typing directly from raw Illumina reads',
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287 formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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288 parser.add_argument('--version', help='Version information', action='version',
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289 version='{prog} v{version}'.format(prog=parser.prog, version=__version__))
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290
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291 parser_required = parser.add_argument_group('Required options')
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292 parser_required.add_argument('-f', '--fastq', nargs='+', action=utils.required_length((1, 2), '--fastq'),
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293 type=argparse.FileType('r'), metavar=('/path/to/input/file.fq.gz'),
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294 help='Path to single OR paired-end fastq files. If two files are passed, they will be'
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295 ' assumed as being the paired fastq files', required=True)
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296 parser_required.add_argument('-s', '--species', nargs=2, type=str, metavar=('Yersinia', 'enterocolitica'),
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297 help='Species name', required=True)
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298
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299 parser_optional_general = parser.add_argument_group('General facultative options')
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300 parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/path/to/output/directory/',
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301 help='Path to the directory where the information will be stored',
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302 required=False, default='.')
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303 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use',
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304 required=False, default=1)
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305 parser_optional_general.add_argument('--trueCoverage', action='store_true',
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306 help='Assess true coverage before continue typing')
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307 parser_optional_general.add_argument('--noCheckPoint', action='store_true',
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308 help='Ignore the true coverage checking point')
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309 parser_optional_general.add_argument('--minGeneCoverage', type=int, metavar='N',
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310 help='Minimum typing percentage of target reference gene sequence covered to'
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311 ' consider a gene to be present (value between [0, 100])', required=False)
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312 parser_optional_general.add_argument('--minGeneIdentity', type=int, metavar='N',
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313 help='Minimum typing percentage of identity of reference gene sequence covered'
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314 ' to consider a gene to be present (value between [0, 100]). One INDEL'
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315 ' will be considered as one difference', required=False)
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316 parser_optional_general.add_argument('--minGeneDepth', type=int, metavar='N',
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317 help='Minimum typing gene average coverage depth of present positions to'
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318 ' consider a gene to be present (default is 1/3 of average sample'
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319 ' coverage or 15x)', required=False)
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320 parser_optional_general.add_argument('--doNotRemoveConsensus', action='store_true',
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321 help='Do not remove ReMatCh consensus sequences')
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322 parser_optional_general.add_argument('--debug', action='store_true',
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323 help='DeBug Mode: do not remove temporary files')
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324
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325 args = parser.parse_args()
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326
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327 if args.minGeneCoverage is not None and (args.minGeneCoverage < 0 or args.minGeneCoverage > 100):
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328 parser.error('--minGeneCoverage should be a value between [0, 100]')
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329 if args.minGeneIdentity is not None and (args.minGeneIdentity < 0 or args.minGeneIdentity > 100):
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330 parser.error('--minGeneIdentity should be a value between [0, 100]')
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331
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332 start_time = time.time()
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333
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334 args.outdir = os.path.abspath(args.outdir)
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335 if not os.path.isdir(args.outdir):
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336 os.makedirs(args.outdir)
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337
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338 # Start logger
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339 logfile, time_str = utils.start_logger(args.outdir)
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340
3
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341 script_path = utils.general_information(logfile, __version__, args.outdir, time_str)
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342 print('\n')
0
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343
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344 rematch = include_rematch_dependencies_path()
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345
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346 args.fastq = [fastq.name for fastq in args.fastq]
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347
3
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348 reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, typing_file, \
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349 typing_sequences, typing_headers, typing_rules, typing_config = \
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350 set_reference(args.species, args.outdir, script_path, args.trueCoverage)
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351 original_reference_file = str(reference_file)
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352
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353 run_successfully, bam_file = mapping_reads(args.fastq, reference_file, args.threads, args.outdir, False, 1)
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354 if run_successfully:
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355 rematch_dir = os.path.join(args.outdir, 'rematch', '')
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356 if not os.path.isdir(rematch_dir):
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357 os.makedirs(rematch_dir)
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358
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359 if args.trueCoverage:
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360 if trueCoverage_file is not None:
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361 trueCoverage_dir = os.path.join(rematch_dir, 'trueCoverage', '')
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362 if not os.path.isdir(trueCoverage_dir):
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363 os.makedirs(trueCoverage_dir)
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364
3
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365 print('\n')
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366 run_successfully, trueCoverage_bam = split_bam(bam_file, trueCoverage_headers, trueCoverage_dir,
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367 args.threads)
0
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368 if run_successfully:
3
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369 run_successfully = indexAlignment(trueCoverage_bam)
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370 if run_successfully:
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371 reference_file = os.path.join(trueCoverage_dir, 'reference.fasta')
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372 write_sequeces(reference_file, trueCoverage_sequences)
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373 index_fasta_samtools(reference_file, None, None, True)
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374 config = parse_config(trueCoverage_config)
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375 runtime, run_successfully, sample_data_general, data_by_gene = \
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376 run_rematch.run_rematch(rematch, trueCoverage_dir, reference_file, trueCoverage_bam,
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377 args.threads, config['length_extra_seq'],
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378 config['minimum_depth_presence'], config['minimum_depth_call'],
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379 config['minimum_depth_frequency_dominant_allele'],
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380 config['minimum_gene_coverage'], config['minimum_gene_identity'],
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381 args.debug, args.doNotRemoveConsensus)
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382
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383 if run_successfully and sample_data_general['mean_sample_coverage'] is not None and \
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384 sample_data_general['number_absent_genes'] is not None and \
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385 sample_data_general['number_genes_multiple_alleles'] is not None:
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386 if args.minGeneDepth is None:
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387 args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \
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388 sample_data_general['mean_sample_coverage'] / 3 > 15 else \
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389 15
0
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390
3
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391 exit_info = []
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392 if sample_data_general['mean_sample_coverage'] < config['minimum_read_coverage']:
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393 exit_info.append('Sample coverage ({mean}) lower than the minimum'
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394 ' required ({minimum})'
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395 ''.format(mean=sample_data_general['mean_sample_coverage'],
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396 minimum=config['minimum_read_coverage']))
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397 if sample_data_general['number_absent_genes'] > config['maximum_number_absent_genes']:
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398 exit_info.append('Number of absent genes ({number}) higher than the'
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399 ' maximum allowed ({maximum})'
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400 ''.format(number=sample_data_general['number_absent_genes'],
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401 maximum=config['maximum_number_absent_genes']))
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402 if sample_data_general['number_genes_multiple_alleles'] > \
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403 config['maximum_number_genes_multiple_alleles']:
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404 exit_info.append('Number of genes with multiple alleles'
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405 ' ({number}) higher than the maximum'
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406 ' allowed ({maximum})'
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407 ''.format(number=sample_data_general['number_genes_multiple_alleles'],
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408 maximum=config['maximum_number_genes_multiple_alleles']))
0
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409
3
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410 if len(exit_info) > 0:
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411 print('\n' + '\n'.join(exit_info) + '\n')
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412 e = 'TrueCoverage requirements not fulfilled'
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413 print('\n' + e + '\n')
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414 if not args.noCheckPoint:
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415 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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416 _ = utils.runTime(start_time)
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417 sys.exit(e)
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418 else:
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419 e = 'TrueCoverage module did not run successfully'
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420 print('\n' + e + '\n')
0
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421 if not args.noCheckPoint:
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422 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
3
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423 _ = utils.runTime(start_time)
0
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424 sys.exit(e)
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425
3
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426 print('\n')
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427 typing_dir = os.path.join(rematch_dir, 'typing', '')
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428 if not os.path.isdir(typing_dir):
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429 os.makedirs(typing_dir)
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430 run_successfully, bam_file = split_bam(bam_file, typing_headers, typing_dir, args.threads)
0
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431 if run_successfully:
3
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432 run_successfully = indexAlignment(bam_file)
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433 if run_successfully:
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434 reference_file = os.path.join(typing_dir, 'reference.fasta')
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435 write_sequeces(reference_file, typing_sequences)
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436 index_fasta_samtools(reference_file, None, None, True)
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437 rematch_dir = str(typing_dir)
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438 if not run_successfully:
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439 if args.noCheckPoint:
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440 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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441 _ = utils.runTime(start_time)
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442 sys.exit('Something in the required TrueCoverage analysis went wrong')
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443 else:
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444 print('\n'
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445 'WARNING: it was not found trueCoverage target files. trueCoverage will not run.'
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446 '\n')
0
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447
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448 if run_successfully:
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449 config = parse_config(typing_config)
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450 if args.minGeneCoverage is not None:
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451 config['minimum_gene_coverage'] = args.minGeneCoverage
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452 if args.minGeneIdentity is not None:
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453 config['minimum_gene_identity'] = args.minGeneIdentity
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454
3
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455 runtime, run_successfully, sample_data_general, data_by_gene = \
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456 run_rematch.run_rematch(rematch, rematch_dir, reference_file, bam_file, args.threads,
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457 config['length_extra_seq'], config['minimum_depth_presence'],
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458 config['minimum_depth_call'], config['minimum_depth_frequency_dominant_allele'],
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459 config['minimum_gene_coverage'], config['minimum_gene_identity'],
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460 args.debug, args.doNotRemoveConsensus)
0
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461 if run_successfully and data_by_gene is not None:
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462 if args.minGeneDepth is None:
3
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463 args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \
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464 sample_data_general['mean_sample_coverage'] / 3 > 15 else \
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465 15
0
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466 else:
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467 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
3
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468 _ = utils.runTime(start_time)
0
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469 sys.exit('ReMatCh run for pathotyping did not run successfully')
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470 else:
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471 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
3
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472 _ = utils.runTime(start_time)
0
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473 sys.exit('Something did not run successfully')
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474
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475 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
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476
3
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477 print('\n')
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478 _ = utils.runTime(start_time)
0
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479
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480
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481 if __name__ == "__main__":
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482 main()