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

planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
1 #!/usr/bin/env python3
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
2
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
3 # -*- coding: utf-8 -*-
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
4
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
5 """
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
6 patho_typing.py - In silico pathogenic typing directly from raw
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
7 Illumina reads
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
8 <https://github.com/B-UMMI/patho_typing/>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
9
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
10 Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
11
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
12 Last modified: October 15, 2018
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
13
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
14 This program is free software: you can redistribute it and/or modify
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
15 it under the terms of the GNU General Public License as published by
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
16 the Free Software Foundation, either version 3 of the License, or
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
17 (at your option) any later version.
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
18
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
19 This program is distributed in the hope that it will be useful,
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
20 but WITHOUT ANY WARRANTY; without even the implied warranty of
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
21 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
22 GNU General Public License for more details.
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
23
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
24 You should have received a copy of the GNU General Public License
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
25 along with this program. If not, see <http://www.gnu.org/licenses/>.
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
26
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
27 2020-01-13 ISS
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
28 In order to use the module within the EURL_WGS_Typer pipeline with a
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
29 different virulence database for E coli, mapping against the
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
30 typing_rules.tab was deactivated.
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
31 """
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
32
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
33 import argparse
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
34 import os
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
35 import time
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
36 import sys
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
37 from pkg_resources import resource_filename
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
38
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
39 try:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
40 from __init__ import __version__
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
41
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
42 import modules.utils as utils
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
43 import modules.run_rematch as run_rematch
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
44 import modules.typing as typing
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
45 except ImportError:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
46 from pathotyping.__init__ import __version__
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
47
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
48 from pathotyping.modules import utils as utils
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
49 from pathotyping.modules import run_rematch as run_rematch
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
50 from pathotyping.modules import typing as typing
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
51
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
52
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
53 def set_reference(species, outdir, script_path, trueCoverage):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
54 reference_file = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
55 trueCoverage_file = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
56 trueCoverage_sequences = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
57 trueCoverage_headers = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
58 trueCoverage_config = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
59 typing_file = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
60 typing_sequences = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
61 typing_headers = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
62 typing_rules = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
63 typing_config = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
64
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
65 species_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
66 '_'.join([s.lower() for s in species]), '')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
67
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
68 if os.path.isdir(species_folder):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
69 typing_rules = os.path.join(species_folder, 'typing_rules.tab')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
70 typing_file = os.path.join(species_folder, 'typing.fasta')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
71 typing_sequences, ignore = utils.get_sequence_information(typing_file, 0)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
72 typing_sequences, typing_headers = utils.clean_headers_sequences(typing_sequences)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
73 typing_sequences = utils.simplify_sequence_dict(typing_sequences)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
74 typing_config = os.path.join(species_folder, 'typing.config')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
75 if trueCoverage:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
76 if os.path.isfile(os.path.join(species_folder, 'trueCoverage.fasta')):
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
77 trueCoverage_file = os.path.join(species_folder, 'trueCoverage.fasta')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
78 trueCoverage_sequences, ignore = utils.get_sequence_information(trueCoverage_file, 0)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
79 trueCoverage_sequences, trueCoverage_headers = utils.clean_headers_sequences(trueCoverage_sequences)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
80 trueCoverage_sequences = utils.simplify_sequence_dict(trueCoverage_sequences)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
81 trueCoverage_config = os.path.join(species_folder, 'trueCoverage.config')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
82
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
83 trueCoverage_typing_sequences = trueCoverage_sequences.copy()
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
84 for header in typing_sequences:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
85 if header not in trueCoverage_sequences:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
86 trueCoverage_typing_sequences[header] = typing_sequences[header]
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
87 else:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
88 print('Sequence {header} of typing.fasta already present in'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
89 ' trueCoverage.fasta'.format(header=header))
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
90
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
91 reference_file = os.path.join(outdir, 'trueCoverage_typing.fasta')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
92 write_sequeces(reference_file, trueCoverage_typing_sequences)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
93 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
94 reference_file = os.path.join(outdir, 'typing.fasta')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
95 write_sequeces(reference_file, typing_sequences)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
96 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
97 species_present = []
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
98 seq_conf_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf', '')
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
99 species_folder = [d for d in os.listdir(seq_conf_folder) if
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
100 not d.startswith('.') and os.path.isdir(os.path.join(seq_conf_folder, d, ''))]
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
101 for species in species_folder:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
102 species = species.split('_')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
103 species[0] = species[0][0].upper() + species[0][1:]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
104 species_present.append(' '.join(species))
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
105 sys.exit('Only these species are available:' + '\n' + '\n'.join(species_present))
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
106
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
107 return reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
108 typing_file, typing_sequences, typing_headers, typing_rules, typing_config
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
109
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
110
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
111 def index_fasta_samtools(fasta, region_None, region_outfile_none, print_comand_True):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
112 command = ['samtools', 'faidx', fasta, '', '', '']
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
113 shell_true = False
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
114 if region_None is not None:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
115 command[3] = region_None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
116 if region_outfile_none is not None:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
117 command[4] = '>'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
118 command[5] = region_outfile_none
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
119 shell_true = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
120 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, shell_true, None, print_comand_True)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
121 return run_successfully, stdout
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
122
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
123
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
124 def indexSequenceBowtie2(referenceFile, threads):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
125 if os.path.isfile(str(referenceFile + '.1.bt2')):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
126 run_successfully = True
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
127 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
128 command = ['bowtie2-build', '--threads', str(threads), referenceFile, referenceFile]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
129 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
130 return run_successfully
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
131
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
132
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
133 def run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
134 sam_file = os.path.join(outdir, str('alignment.sam'))
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
135
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
136 run_successfully = indexSequenceBowtie2(referenceFile, threads)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
137 if run_successfully:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
138 command = ['bowtie2', '-k', str(numMapLoc), '-q', '', '--threads', str(threads), '-x', referenceFile, '',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
139 '--no-unal', '-S', sam_file]
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
140
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
141 if len(fastq_files) == 1:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
142 command[9] = '-U ' + fastq_files[0]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
143 elif len(fastq_files) == 2:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
144 command[9] = '-1 ' + fastq_files[0] + ' -2 ' + fastq_files[1]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
145 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
146 return False, None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
147
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
148 if conserved_True:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
149 command[4] = '--sensitive'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
150 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
151 command[4] = '--very-sensitive-local'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
152
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
153 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
154
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
155 if not run_successfully:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
156 sam_file = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
157
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
158 return run_successfully, sam_file
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
159
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
160
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
161 def sortAlignment(alignment_file, output_file, sortByName_True, threads):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
162 outFormat_string = os.path.splitext(output_file)[1][1:].lower()
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
163 command = ['samtools', 'sort', '-o', output_file, '-O', outFormat_string, '', '-@', str(threads), alignment_file]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
164 if sortByName_True:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
165 command[6] = '-n'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
166 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
167 if not run_successfully:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
168 output_file = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
169 return run_successfully, output_file
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
170
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
171
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
172 def indexAlignment(alignment_file):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
173 command = ['samtools', 'index', alignment_file]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
174 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
175 return run_successfully
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
176
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
177
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
178 def mapping_reads(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc):
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
179 print('\n' + 'Mapping the reads' + '\n')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
180 run_successfully, sam_file = run_bowtie(fastq_files, referenceFile, threads, outdir, conserved_True, numMapLoc)
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
181 bam_file = None
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
182 if run_successfully:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
183 run_successfully, bam_file = sortAlignment(sam_file, str(os.path.splitext(sam_file)[0] + '.bam'), False,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
184 threads)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
185 if run_successfully:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
186 os.remove(sam_file)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
187 run_successfully = indexAlignment(bam_file)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
188 if run_successfully:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
189 index_fasta_samtools(referenceFile, None, None, True)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
190 return run_successfully, bam_file
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
191
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
192
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
193 def include_rematch_dependencies_path():
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
194 original_rematch = None
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
195 command = ['which', 'rematch.py']
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
196 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, False)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
197 if run_successfully:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
198 original_rematch = stdout.splitlines()[0]
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
199
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
200 resource_rematch = None
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
201 try:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
202 resource_rematch = resource_filename('ReMatCh', 'rematch.py')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
203 except ModuleNotFoundError:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
204 resource_rematch = original_rematch
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
205 else:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
206 print('\n'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
207 'Using ReMatCh "{resource_rematch}" via "{original_rematch}"\n'.format(resource_rematch=resource_rematch,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
208 original_rematch=original_rematch))
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
209
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
210 if resource_rematch is not None:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
211 utils.setPATHvariable(False, resource_rematch)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
212 else:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
213 sys.exit('ReMatCh not found in the PATH')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
214
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
215 return resource_rematch
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
216
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
217
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
218 def split_bam(bam_file, list_sequences, outdir, threads):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
219 new_bam = os.path.join(outdir, 'partial.bam')
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
220 command = ['samtools', 'view', '-b', '-u', '-h', '-o', new_bam, '-@', str(threads), bam_file,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
221 ' '.join(list_sequences)]
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
222 run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, True)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
223 return run_successfully, new_bam
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
224
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
225
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
226 def parse_config(config_file):
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
227 config = {'reference_file': None, 'length_extra_seq': None, 'maximum_number_absent_genes': None,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
228 'maximum_number_genes_multiple_alleles': None, 'minimum_read_coverage': None,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
229 'minimum_depth_presence': None, 'minimum_depth_call': None,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
230 'minimum_depth_frequency_dominant_allele': None, 'minimum_gene_coverage': None,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
231 'minimum_gene_identity': None}
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
232
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
233 with open(config_file, 'rt') as reader:
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
234 field = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
235 for line in reader:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
236 line = line.splitlines()[0]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
237 if len(line) > 0:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
238 line = line.split(' ')[0]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
239 if line.startswith('#'):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
240 line = line[1:].split(' ')[0]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
241 field = line
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
242 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
243 if field is not None:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
244 if field in ['length_extra_seq', 'maximum_number_absent_genes',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
245 'maximum_number_genes_multiple_alleles', 'minimum_read_coverage',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
246 'minimum_depth_presence', 'minimum_depth_call', 'minimum_gene_coverage',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
247 'minimum_gene_identity']:
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
248 line = int(line)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
249 if field in ['minimum_gene_coverage', 'minimum_gene_identity']:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
250 if line < 0 or line > 100:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
251 sys.exit('minimum_gene_coverage in trueCoverage_rematch config file must be an'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
252 ' integer between 0 and 100')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
253 elif field == 'minimum_depth_frequency_dominant_allele':
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
254 line = float(line)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
255 if line < 0 or line > 1:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
256 sys.exit('minimum_depth_frequency_dominant_allele in trueCoverage_rematch config file'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
257 ' must be a double between 0 and 1')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
258 config[field] = line
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
259 field = None
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
260
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
261 for field in config:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
262 if config[field] is None:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
263 sys.exit(field + ' in trueCoverage_rematch config file is missing')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
264
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
265 return config
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
266
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
267
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
268 def clean_pathotyping_folder(outdir, reference_file, debug_mode_true):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
269 if not debug_mode_true:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
270 files = [f for f in os.listdir(outdir) if not f.startswith('.') and os.path.isfile(os.path.join(outdir, f))]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
271 for file_found in files:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
272 if file_found.startswith(('alignment.', os.path.splitext(os.path.basename(reference_file))[0])):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
273 file_found = os.path.join(outdir, file_found)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
274 os.remove(file_found)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
275
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
276
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
277 def write_sequeces(out_file, sequences_dict):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
278 with open(out_file, 'wt') as writer:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
279 for header in sequences_dict:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
280 writer.write('>' + header + '\n')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
281 writer.write('\n'.join(utils.chunkstring(sequences_dict[header]['sequence'], 80)) + '\n')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
282
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
283
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
284 def main():
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
285 parser = argparse.ArgumentParser(prog='patho_typing.py',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
286 description='In silico pathogenic typing directly from raw Illumina reads',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
287 formatter_class=argparse.ArgumentDefaultsHelpFormatter)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
288 parser.add_argument('--version', help='Version information', action='version',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
289 version='{prog} v{version}'.format(prog=parser.prog, version=__version__))
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
290
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
291 parser_required = parser.add_argument_group('Required options')
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
292 parser_required.add_argument('-f', '--fastq', nargs='+', action=utils.required_length((1, 2), '--fastq'),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
293 type=argparse.FileType('r'), metavar=('/path/to/input/file.fq.gz'),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
294 help='Path to single OR paired-end fastq files. If two files are passed, they will be'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
295 ' assumed as being the paired fastq files', required=True)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
296 parser_required.add_argument('-s', '--species', nargs=2, type=str, metavar=('Yersinia', 'enterocolitica'),
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
297 help='Species name', required=True)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
298
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
299 parser_optional_general = parser.add_argument_group('General facultative options')
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
300 parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/path/to/output/directory/',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
301 help='Path to the directory where the information will be stored',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
302 required=False, default='.')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
303 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
304 required=False, default=1)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
305 parser_optional_general.add_argument('--trueCoverage', action='store_true',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
306 help='Assess true coverage before continue typing')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
307 parser_optional_general.add_argument('--noCheckPoint', action='store_true',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
308 help='Ignore the true coverage checking point')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
309 parser_optional_general.add_argument('--minGeneCoverage', type=int, metavar='N',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
310 help='Minimum typing percentage of target reference gene sequence covered to'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
311 ' consider a gene to be present (value between [0, 100])', required=False)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
312 parser_optional_general.add_argument('--minGeneIdentity', type=int, metavar='N',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
313 help='Minimum typing percentage of identity of reference gene sequence covered'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
314 ' to consider a gene to be present (value between [0, 100]). One INDEL'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
315 ' will be considered as one difference', required=False)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
316 parser_optional_general.add_argument('--minGeneDepth', type=int, metavar='N',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
317 help='Minimum typing gene average coverage depth of present positions to'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
318 ' consider a gene to be present (default is 1/3 of average sample'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
319 ' coverage or 15x)', required=False)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
320 parser_optional_general.add_argument('--doNotRemoveConsensus', action='store_true',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
321 help='Do not remove ReMatCh consensus sequences')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
322 parser_optional_general.add_argument('--debug', action='store_true',
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
323 help='DeBug Mode: do not remove temporary files')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
324
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
325 args = parser.parse_args()
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
326
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
327 if args.minGeneCoverage is not None and (args.minGeneCoverage < 0 or args.minGeneCoverage > 100):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
328 parser.error('--minGeneCoverage should be a value between [0, 100]')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
329 if args.minGeneIdentity is not None and (args.minGeneIdentity < 0 or args.minGeneIdentity > 100):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
330 parser.error('--minGeneIdentity should be a value between [0, 100]')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
331
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
332 start_time = time.time()
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
333
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
334 args.outdir = os.path.abspath(args.outdir)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
335 if not os.path.isdir(args.outdir):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
336 os.makedirs(args.outdir)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
337
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
338 # Start logger
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
339 logfile, time_str = utils.start_logger(args.outdir)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
340
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
341 script_path = utils.general_information(logfile, __version__, args.outdir, time_str)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
342 print('\n')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
343
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
344 rematch = include_rematch_dependencies_path()
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
345
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
346 args.fastq = [fastq.name for fastq in args.fastq]
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
347
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
348 reference_file, trueCoverage_file, trueCoverage_sequences, trueCoverage_headers, trueCoverage_config, typing_file, \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
349 typing_sequences, typing_headers, typing_rules, typing_config = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
350 set_reference(args.species, args.outdir, script_path, args.trueCoverage)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
351 original_reference_file = str(reference_file)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
352
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
353 run_successfully, bam_file = mapping_reads(args.fastq, reference_file, args.threads, args.outdir, False, 1)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
354 if run_successfully:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
355 rematch_dir = os.path.join(args.outdir, 'rematch', '')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
356 if not os.path.isdir(rematch_dir):
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
357 os.makedirs(rematch_dir)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
358
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
359 if args.trueCoverage:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
360 if trueCoverage_file is not None:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
361 trueCoverage_dir = os.path.join(rematch_dir, 'trueCoverage', '')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
362 if not os.path.isdir(trueCoverage_dir):
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
363 os.makedirs(trueCoverage_dir)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
364
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
365 print('\n')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
366 run_successfully, trueCoverage_bam = split_bam(bam_file, trueCoverage_headers, trueCoverage_dir,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
367 args.threads)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
368 if run_successfully:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
369 run_successfully = indexAlignment(trueCoverage_bam)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
370 if run_successfully:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
371 reference_file = os.path.join(trueCoverage_dir, 'reference.fasta')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
372 write_sequeces(reference_file, trueCoverage_sequences)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
373 index_fasta_samtools(reference_file, None, None, True)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
374 config = parse_config(trueCoverage_config)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
375 runtime, run_successfully, sample_data_general, data_by_gene = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
376 run_rematch.run_rematch(rematch, trueCoverage_dir, reference_file, trueCoverage_bam,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
377 args.threads, config['length_extra_seq'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
378 config['minimum_depth_presence'], config['minimum_depth_call'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
379 config['minimum_depth_frequency_dominant_allele'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
380 config['minimum_gene_coverage'], config['minimum_gene_identity'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
381 args.debug, args.doNotRemoveConsensus)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
382
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
383 if run_successfully and sample_data_general['mean_sample_coverage'] is not None and \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
384 sample_data_general['number_absent_genes'] is not None and \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
385 sample_data_general['number_genes_multiple_alleles'] is not None:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
386 if args.minGeneDepth is None:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
387 args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
388 sample_data_general['mean_sample_coverage'] / 3 > 15 else \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
389 15
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
390
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
391 exit_info = []
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
392 if sample_data_general['mean_sample_coverage'] < config['minimum_read_coverage']:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
393 exit_info.append('Sample coverage ({mean}) lower than the minimum'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
394 ' required ({minimum})'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
395 ''.format(mean=sample_data_general['mean_sample_coverage'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
396 minimum=config['minimum_read_coverage']))
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
397 if sample_data_general['number_absent_genes'] > config['maximum_number_absent_genes']:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
398 exit_info.append('Number of absent genes ({number}) higher than the'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
399 ' maximum allowed ({maximum})'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
400 ''.format(number=sample_data_general['number_absent_genes'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
401 maximum=config['maximum_number_absent_genes']))
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
402 if sample_data_general['number_genes_multiple_alleles'] > \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
403 config['maximum_number_genes_multiple_alleles']:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
404 exit_info.append('Number of genes with multiple alleles'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
405 ' ({number}) higher than the maximum'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
406 ' allowed ({maximum})'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
407 ''.format(number=sample_data_general['number_genes_multiple_alleles'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
408 maximum=config['maximum_number_genes_multiple_alleles']))
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
409
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
410 if len(exit_info) > 0:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
411 print('\n' + '\n'.join(exit_info) + '\n')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
412 e = 'TrueCoverage requirements not fulfilled'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
413 print('\n' + e + '\n')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
414 if not args.noCheckPoint:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
415 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
416 _ = utils.runTime(start_time)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
417 sys.exit(e)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
418 else:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
419 e = 'TrueCoverage module did not run successfully'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
420 print('\n' + e + '\n')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
421 if not args.noCheckPoint:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
422 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
423 _ = utils.runTime(start_time)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
424 sys.exit(e)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
425
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
426 print('\n')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
427 typing_dir = os.path.join(rematch_dir, 'typing', '')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
428 if not os.path.isdir(typing_dir):
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
429 os.makedirs(typing_dir)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
430 run_successfully, bam_file = split_bam(bam_file, typing_headers, typing_dir, args.threads)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
431 if run_successfully:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
432 run_successfully = indexAlignment(bam_file)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
433 if run_successfully:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
434 reference_file = os.path.join(typing_dir, 'reference.fasta')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
435 write_sequeces(reference_file, typing_sequences)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
436 index_fasta_samtools(reference_file, None, None, True)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
437 rematch_dir = str(typing_dir)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
438 if not run_successfully:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
439 if args.noCheckPoint:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
440 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
441 _ = utils.runTime(start_time)
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
442 sys.exit('Something in the required TrueCoverage analysis went wrong')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
443 else:
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
444 print('\n'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
445 'WARNING: it was not found trueCoverage target files. trueCoverage will not run.'
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
446 '\n')
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
447
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
448 if run_successfully:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
449 config = parse_config(typing_config)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
450 if args.minGeneCoverage is not None:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
451 config['minimum_gene_coverage'] = args.minGeneCoverage
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
452 if args.minGeneIdentity is not None:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
453 config['minimum_gene_identity'] = args.minGeneIdentity
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
454
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
455 runtime, run_successfully, sample_data_general, data_by_gene = \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
456 run_rematch.run_rematch(rematch, rematch_dir, reference_file, bam_file, args.threads,
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
457 config['length_extra_seq'], config['minimum_depth_presence'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
458 config['minimum_depth_call'], config['minimum_depth_frequency_dominant_allele'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
459 config['minimum_gene_coverage'], config['minimum_gene_identity'],
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
460 args.debug, args.doNotRemoveConsensus)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
461 if run_successfully and data_by_gene is not None:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
462 if args.minGeneDepth is None:
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
463 args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
464 sample_data_general['mean_sample_coverage'] / 3 > 15 else \
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
465 15
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
466 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
467 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
468 _ = utils.runTime(start_time)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
469 sys.exit('ReMatCh run for pathotyping did not run successfully')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
470 else:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
471 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
472 _ = utils.runTime(start_time)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
473 sys.exit('Something did not run successfully')
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
474
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
475 clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
476
3
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
477 print('\n')
0cbed1c0a762 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
478 _ = utils.runTime(start_time)
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
479
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
480
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
481 if __name__ == "__main__":
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
482 main()