Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.2.1/bin/check_samplesheet.py @ 0:77494b0fa3c7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Mon, 27 Jun 2022 15:55:37 -0400
parents
children
rev   line source
kkonganti@0 1 #!/usr/bin/env python3
kkonganti@0 2
kkonganti@0 3 import os
kkonganti@0 4 import sys
kkonganti@0 5 import errno
kkonganti@0 6 import argparse
kkonganti@0 7
kkonganti@0 8
kkonganti@0 9 def parse_args(args=None):
kkonganti@0 10 Description = "Reformat samplesheet file and check its contents."
kkonganti@0 11 Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
kkonganti@0 12
kkonganti@0 13 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
kkonganti@0 14 parser.add_argument("FILE_IN", help="Input samplesheet file.")
kkonganti@0 15 parser.add_argument("FILE_OUT", help="Output file.")
kkonganti@0 16 return parser.parse_args(args)
kkonganti@0 17
kkonganti@0 18
kkonganti@0 19 def make_dir(path):
kkonganti@0 20 if len(path) > 0:
kkonganti@0 21 try:
kkonganti@0 22 os.makedirs(path)
kkonganti@0 23 except OSError as exception:
kkonganti@0 24 if exception.errno != errno.EEXIST:
kkonganti@0 25 raise exception
kkonganti@0 26
kkonganti@0 27
kkonganti@0 28 def print_error(error, context="Line", context_str=""):
kkonganti@0 29 error_str = f"ERROR: Please check samplesheet -> {error}"
kkonganti@0 30 if context != "" and context_str != "":
kkonganti@0 31 error_str = f"ERROR: Please check samplesheet -> {error}\n{context.strip()}: '{context_str.strip()}'"
kkonganti@0 32 print(error_str)
kkonganti@0 33 sys.exit(1)
kkonganti@0 34
kkonganti@0 35
kkonganti@0 36 def check_samplesheet(file_in, file_out):
kkonganti@0 37 """
kkonganti@0 38 This function checks that the samplesheet follows the following structure:
kkonganti@0 39
kkonganti@0 40 sample,fq1,fq2,strandedness
kkonganti@0 41 SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz,forward
kkonganti@0 42 SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz,forward
kkonganti@0 43 SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq,,forward
kkonganti@0 44 SAMPLE_SE,SAMPLE_SE_RUN1_2.fastq.gz,,forward
kkonganti@0 45
kkonganti@0 46 For an example see:
kkonganti@0 47 https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.1/samplesheet_test.csv
kkonganti@0 48 """
kkonganti@0 49
kkonganti@0 50 sample_mapping_dict = {}
kkonganti@0 51 with open(file_in, "r", encoding='utf-8-sig') as fin:
kkonganti@0 52
kkonganti@0 53 ## Check header
kkonganti@0 54 MIN_COLS = 3
kkonganti@0 55 HEADER = ["sample", "fq1", "fq2", "strandedness"]
kkonganti@0 56 header = [x.strip('"') for x in fin.readline().strip().split(",")]
kkonganti@0 57 if header[: len(HEADER)] != HEADER:
kkonganti@0 58 print(
kkonganti@0 59 f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}"
kkonganti@0 60 )
kkonganti@0 61 sys.exit(1)
kkonganti@0 62
kkonganti@0 63 ## Check sample entries
kkonganti@0 64 for line in fin:
kkonganti@0 65 if line.strip():
kkonganti@0 66 lspl = [x.strip().strip('"') for x in line.strip().split(",")]
kkonganti@0 67
kkonganti@0 68 ## Check valid number of columns per row
kkonganti@0 69 if len(lspl) < len(HEADER):
kkonganti@0 70 print_error(
kkonganti@0 71 f"Invalid number of columns (minimum = {len(HEADER)})!",
kkonganti@0 72 "Line",
kkonganti@0 73 line,
kkonganti@0 74 )
kkonganti@0 75
kkonganti@0 76 num_cols = len([x for x in lspl if x])
kkonganti@0 77 if num_cols < MIN_COLS:
kkonganti@0 78 print_error(
kkonganti@0 79 f"Invalid number of populated columns (minimum = {MIN_COLS})!",
kkonganti@0 80 "Line",
kkonganti@0 81 line,
kkonganti@0 82 )
kkonganti@0 83
kkonganti@0 84 ## Check sample name entries
kkonganti@0 85 sample, fq1, fq2, strandedness = lspl[: len(HEADER)]
kkonganti@0 86 if sample.find(" ") != -1:
kkonganti@0 87 print(
kkonganti@0 88 f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
kkonganti@0 89 )
kkonganti@0 90 sample = sample.replace(" ", "_")
kkonganti@0 91 if not sample:
kkonganti@0 92 print_error("Sample entry has not been specified!", "Line", line)
kkonganti@0 93
kkonganti@0 94 ## Check FastQ file extension
kkonganti@0 95 for fastq in [fq1, fq2]:
kkonganti@0 96 if fastq:
kkonganti@0 97 if fastq.find(" ") != -1:
kkonganti@0 98 print_error("FastQ file contains spaces!", "Line", line)
kkonganti@0 99 # if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
kkonganti@0 100 # print_error(
kkonganti@0 101 # "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
kkonganti@0 102 # "Line",
kkonganti@0 103 # line,
kkonganti@0 104 # )
kkonganti@0 105
kkonganti@0 106 ## Check strandedness
kkonganti@0 107 strandednesses = ["unstranded", "forward", "reverse"]
kkonganti@0 108 if strandedness:
kkonganti@0 109 if strandedness not in strandednesses:
kkonganti@0 110 print_error(
kkonganti@0 111 f"Strandedness must be one of '{', '.join(strandednesses)}'!",
kkonganti@0 112 "Line",
kkonganti@0 113 line,
kkonganti@0 114 )
kkonganti@0 115 else:
kkonganti@0 116 print_error(
kkonganti@0 117 f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.",
kkonganti@0 118 "Line",
kkonganti@0 119 line,
kkonganti@0 120 )
kkonganti@0 121
kkonganti@0 122 ## Auto-detect paired-end/single-end
kkonganti@0 123 sample_info = [] ## [single_end, fq1, fq2, strandedness]
kkonganti@0 124 if sample and fq1 and fq2: ## Paired-end short reads
kkonganti@0 125 sample_info = ["0", fq1, fq2, strandedness]
kkonganti@0 126 elif sample and fq1 and not fq2: ## Single-end short reads
kkonganti@0 127 sample_info = ["1", fq1, fq2, strandedness]
kkonganti@0 128 else:
kkonganti@0 129 print_error("Invalid combination of columns provided!", "Line", line)
kkonganti@0 130
kkonganti@0 131 ## Create sample mapping dictionary = {sample: [[ single_end, fq1, fq2, strandedness ]]}
kkonganti@0 132 if sample not in sample_mapping_dict:
kkonganti@0 133 sample_mapping_dict[sample] = [sample_info]
kkonganti@0 134 else:
kkonganti@0 135 if sample_info in sample_mapping_dict[sample]:
kkonganti@0 136 print_error("Samplesheet contains duplicate rows!", "Line", line)
kkonganti@0 137 else:
kkonganti@0 138 sample_mapping_dict[sample].append(sample_info)
kkonganti@0 139
kkonganti@0 140 ## Write validated samplesheet with appropriate columns
kkonganti@0 141 if len(sample_mapping_dict) > 0:
kkonganti@0 142 out_dir = os.path.dirname(file_out)
kkonganti@0 143 make_dir(out_dir)
kkonganti@0 144 with open(file_out, "w") as fout:
kkonganti@0 145 fout.write(
kkonganti@0 146 ",".join(["sample", "single_end", "fq1", "fq2", "strandedness"])
kkonganti@0 147 + "\n"
kkonganti@0 148 )
kkonganti@0 149 for sample in sorted(sample_mapping_dict.keys()):
kkonganti@0 150
kkonganti@0 151 ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
kkonganti@0 152 if not all(
kkonganti@0 153 x[0] == sample_mapping_dict[sample][0][0]
kkonganti@0 154 for x in sample_mapping_dict[sample]
kkonganti@0 155 ):
kkonganti@0 156 print_error(
kkonganti@0 157 f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!",
kkonganti@0 158 "Sample",
kkonganti@0 159 sample,
kkonganti@0 160 )
kkonganti@0 161
kkonganti@0 162 ## Check that multiple runs of the same sample are of the same strandedness
kkonganti@0 163 if not all(
kkonganti@0 164 x[-1] == sample_mapping_dict[sample][0][-1]
kkonganti@0 165 for x in sample_mapping_dict[sample]
kkonganti@0 166 ):
kkonganti@0 167 print_error(
kkonganti@0 168 f"Multiple runs of a sample must have the same strandedness!",
kkonganti@0 169 "Sample",
kkonganti@0 170 sample,
kkonganti@0 171 )
kkonganti@0 172
kkonganti@0 173 for idx, val in enumerate(sample_mapping_dict[sample]):
kkonganti@0 174 fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
kkonganti@0 175 else:
kkonganti@0 176 print_error(f"No entries to process!", "Samplesheet: {file_in}")
kkonganti@0 177
kkonganti@0 178
kkonganti@0 179 def main(args=None):
kkonganti@0 180 args = parse_args(args)
kkonganti@0 181 check_samplesheet(args.FILE_IN, args.FILE_OUT)
kkonganti@0 182
kkonganti@0 183
kkonganti@0 184 if __name__ == "__main__":
kkonganti@0 185 sys.exit(main())