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