Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.5.0/bin/check_samplesheet.py @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 #!/usr/bin/env python3
2
3 import os
4 import sys
5 import errno
6 import argparse
7
8
9 def parse_args(args=None):
10 Description = "Reformat samplesheet file and check its contents."
11 Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
12
13 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
14 parser.add_argument("FILE_IN", help="Input samplesheet file.")
15 parser.add_argument("FILE_OUT", help="Output file.")
16 return parser.parse_args(args)
17
18
19 def make_dir(path):
20 if len(path) > 0:
21 try:
22 os.makedirs(path)
23 except OSError as exception:
24 if exception.errno != errno.EEXIST:
25 raise exception
26
27
28 def print_error(error, context="Line", context_str=""):
29 error_str = f"ERROR: Please check samplesheet -> {error}"
30 if context != "" and context_str != "":
31 error_str = f"ERROR: Please check samplesheet -> {error}\n{context.strip()}: '{context_str.strip()}'"
32 print(error_str)
33 sys.exit(1)
34
35
36 def check_samplesheet(file_in, file_out):
37 """
38 This function checks that the samplesheet follows the following structure:
39
40 sample,fq1,fq2,strandedness
41 SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz,forward
42 SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz,forward
43 SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq,,forward
44 SAMPLE_SE,SAMPLE_SE_RUN1_2.fastq.gz,,forward
45
46 For an example see:
47 https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.1/samplesheet_test.csv
48 """
49
50 sample_mapping_dict = {}
51 with open(file_in, "r", encoding='utf-8-sig') as fin:
52
53 ## Check header
54 MIN_COLS = 3
55 HEADER = ["sample", "fq1", "fq2", "strandedness"]
56 header = [x.strip('"') for x in fin.readline().strip().split(",")]
57 if header[: len(HEADER)] != HEADER:
58 print(
59 f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}"
60 )
61 sys.exit(1)
62
63 ## Check sample entries
64 for line in fin:
65 if line.strip():
66 lspl = [x.strip().strip('"') for x in line.strip().split(",")]
67
68 ## Check valid number of columns per row
69 if len(lspl) < len(HEADER):
70 print_error(
71 f"Invalid number of columns (minimum = {len(HEADER)})!",
72 "Line",
73 line,
74 )
75
76 num_cols = len([x for x in lspl if x])
77 if num_cols < MIN_COLS:
78 print_error(
79 f"Invalid number of populated columns (minimum = {MIN_COLS})!",
80 "Line",
81 line,
82 )
83
84 ## Check sample name entries
85 sample, fq1, fq2, strandedness = lspl[: len(HEADER)]
86 if sample.find(" ") != -1:
87 print(
88 f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
89 )
90 sample = sample.replace(" ", "_")
91 if not sample:
92 print_error("Sample entry has not been specified!", "Line", line)
93
94 ## Check FastQ file extension
95 for fastq in [fq1, fq2]:
96 if fastq:
97 if fastq.find(" ") != -1:
98 print_error("FastQ file contains spaces!", "Line", line)
99 # if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
100 # print_error(
101 # "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
102 # "Line",
103 # line,
104 # )
105
106 ## Check strandedness
107 strandednesses = ["unstranded", "forward", "reverse"]
108 if strandedness:
109 if strandedness not in strandednesses:
110 print_error(
111 f"Strandedness must be one of '{', '.join(strandednesses)}'!",
112 "Line",
113 line,
114 )
115 else:
116 print_error(
117 f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.",
118 "Line",
119 line,
120 )
121
122 ## Auto-detect paired-end/single-end
123 sample_info = [] ## [single_end, fq1, fq2, strandedness]
124 if sample and fq1 and fq2: ## Paired-end short reads
125 sample_info = ["0", fq1, fq2, strandedness]
126 elif sample and fq1 and not fq2: ## Single-end short reads
127 sample_info = ["1", fq1, fq2, strandedness]
128 else:
129 print_error("Invalid combination of columns provided!", "Line", line)
130
131 ## Create sample mapping dictionary = {sample: [[ single_end, fq1, fq2, strandedness ]]}
132 if sample not in sample_mapping_dict:
133 sample_mapping_dict[sample] = [sample_info]
134 else:
135 if sample_info in sample_mapping_dict[sample]:
136 print_error("Samplesheet contains duplicate rows!", "Line", line)
137 else:
138 sample_mapping_dict[sample].append(sample_info)
139
140 ## Write validated samplesheet with appropriate columns
141 if len(sample_mapping_dict) > 0:
142 out_dir = os.path.dirname(file_out)
143 make_dir(out_dir)
144 with open(file_out, "w") as fout:
145 fout.write(
146 ",".join(["sample", "single_end", "fq1", "fq2", "strandedness"])
147 + "\n"
148 )
149 for sample in sorted(sample_mapping_dict.keys()):
150
151 ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
152 if not all(
153 x[0] == sample_mapping_dict[sample][0][0]
154 for x in sample_mapping_dict[sample]
155 ):
156 print_error(
157 f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!",
158 "Sample",
159 sample,
160 )
161
162 ## Check that multiple runs of the same sample are of the same strandedness
163 if not all(
164 x[-1] == sample_mapping_dict[sample][0][-1]
165 for x in sample_mapping_dict[sample]
166 ):
167 print_error(
168 f"Multiple runs of a sample must have the same strandedness!",
169 "Sample",
170 sample,
171 )
172
173 for idx, val in enumerate(sample_mapping_dict[sample]):
174 fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
175 else:
176 print_error(f"No entries to process!", "Samplesheet: {file_in}")
177
178
179 def main(args=None):
180 args = parse_args(args)
181 check_samplesheet(args.FILE_IN, args.FILE_OUT)
182
183
184 if __name__ == "__main__":
185 sys.exit(main())