Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
#!/usr/bin/env python3
'''Check if design file is correctly formatted and matches files list.'''
import argparse
import logging
import pandas as pd
EPILOG = '''
For more details:
%(prog)s --help
'''
## SETTINGS
logger = logging.getLogger(__name__)
logger.addHandler(logging.NullHandler())
logger.propagate = False
logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-d', '--design',
help="The design file to run QC (TSV format).",
required=True)
parser.add_argument('-f', '--fastq',
help="File with list of fastq files (csv format).",
required=True)
parser.add_argument('-p', '--paired',
help="True/False if paired-end or single end.",
default=True,
action='store_true')
args = parser.parse_args()
return args
def check_design_headers(design, paired):
'''Check if design file conforms to sequencing type.'''
# Default headers
design_template = [
'sample_id',
'biosample',
'factor',
'treatment',
'replicate',
'control_id',
'fastq_read1']
design_headers = list(design.columns.values)
if paired: # paired-end data
design_template.extend(['fastq_read2'])
# Check if headers
logger.info("Running header check.")
missing_headers = set(design_template) - set(design_headers)
if len(missing_headers) > 0:
logger.error('Missing column headers: %s', list(missing_headers))
raise Exception("Missing column headers: %s" % list(missing_headers))
def check_controls(design):
'''Check if design file has the correct control mapping.'''
logger.info("Running control check.")
missing_controls = set(design['control_id']) - set(design['sample_id'])
if len(missing_controls) > 0:
logger.error('Missing control experiments: %s', list(missing_controls))
raise Exception("Missing control experiments: %s" % list(missing_controls))
def check_files(design, fastq, paired):
'''Check if design file has the files found.'''
logger.info("Running file check.")
if paired: # paired-end data
files = list(design['fastq_read1']) + list(design['fastq_read2'])
else: # single-end data
files = design['fastq_read1']
files_found = fastq['name']
missing_files = set(files) - set(files_found)
if len(missing_files) > 0:
logger.error('Missing files from design file: %s', list(missing_files))
raise Exception("Missing files from design file: %s" % list(missing_files))
else:
file_dict = fastq.set_index('name').T.to_dict()
design['fastq_read1'] = design['fastq_read1'] \
.apply(lambda x: file_dict[x]['path'])
if paired: # paired-end data
design['fastq_read2'] = design['fastq_read2'] \
.apply(lambda x: file_dict[x]['path'])
return design
def main():
args = get_args()
# Create a file handler
handler = logging.FileHandler('design.log')
logger.addHandler(handler)
# Read files
design_file = pd.read_csv(args.design, sep='\t')
fastq_file = pd.read_csv(args.design, sep='\t', names=['name', 'path'])
# Check design file
check_design_headers(design_file, args.paired)
check_controls(design_file)
new_design = check_files(design_file, fastq_file, args.paired)
# Write out new design file
new_design.to_csv('design.tsv', header=True, index=False)
if __name__ == '__main__':
main()