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https://github.com/MillironX/taxprofiler.git
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add more columns to samplesheet
This commit is contained in:
maxibor
parent
12e7b428f2
commit
f867c057a4
1 changed files with 118 additions and 20 deletions
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@ -3,6 +3,7 @@
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# TODO nf-core: Update the script to check the samplesheet
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# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
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from distutils import extension
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import os
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import sys
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import errno
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@ -10,7 +11,9 @@ import argparse
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def parse_args(args=None):
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Description = "Reformat nf-core/taxprofiler samplesheet file and check its contents."
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Description = (
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"Reformat nf-core/taxprofiler samplesheet file and check its contents."
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)
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Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
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parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
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@ -43,25 +46,62 @@ def check_samplesheet(file_in, file_out):
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"""
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This function checks that the samplesheet follows the following structure:
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sample,fastq_1,fastq_2
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SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
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SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
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SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
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sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
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2611,ERR5766174,ILLUMINA,NA,NA,FA_EXTENSIONSERX5474930_ERR5766174_1.fa.gz
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2612,ERR5766176,ILLUMINA,ERX5474932_ERR5766176_1.fastq.gz,ERX5474932_ERR5766176_2.fastq.gz,NA
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2612,ERR5766174,ILLUMINA,ERX5474936_ERR5766180_1.fastq.gz,NA,NA
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2613,ERR5766181,ILLUMINA,ERX5474930_ERR5766174_1.fa.gz,ERX5474930_ERR5766174_2.fa.gz,NA
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For an example see:
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https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
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"""
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FQ_EXTENSIONS = (".fq", ".fq.gz", ".fastq", ".fastq.gz")
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FA_EXTENSIONS = (
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".fa",
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".fa.gz",
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".fasta",
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".fasta.gz",
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".fna",
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".fna.gz",
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".fas",
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".fas.gz",
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)
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INSTRUMENT_PLATFORMS = [
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"ABI_SOLID",
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"BGISEQ",
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"CAPILLARY",
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"COMPLETE_GENOMICS",
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"DNBSEQ",
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"HELICOS",
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"ILLUMINA",
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"ION_TORRENT",
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"LS454",
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"OXFORD_NANOPORE",
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"PACBIO_SMRT",
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]
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sample_mapping_dict = {}
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with open(file_in, "r") as fin:
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## Check header
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MIN_COLS = 2
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MIN_COLS = 4
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# TODO nf-core: Update the column names for the input samplesheet
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HEADER = ["sample", "fastq_1", "fastq_2"]
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HEADER = [
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"sample",
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"run_accession",
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"instrument_platform",
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"fastq_1",
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"fastq_2",
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"fasta",
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]
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header = [x.strip('"') for x in fin.readline().strip().split(",")]
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if header[: len(HEADER)] != HEADER:
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print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER)))
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print(
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"ERROR: Please check samplesheet header -> {} != {}".format(
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",".join(header), ",".join(HEADER)
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)
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)
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sys.exit(1)
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## Check sample entries
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@ -78,13 +118,22 @@ def check_samplesheet(file_in, file_out):
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num_cols = len([x for x in lspl if x])
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if num_cols < MIN_COLS:
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print_error(
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"Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
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"Invalid number of populated columns (minimum = {})!".format(
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MIN_COLS
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),
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"Line",
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line,
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)
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## Check sample name entries
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sample, fastq_1, fastq_2 = lspl[: len(HEADER)]
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(
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sample,
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run_accession,
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instrument_platform,
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fastq_1,
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fastq_2,
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fasta,
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) = lspl[: len(HEADER)]
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sample = sample.replace(" ", "_")
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if not sample:
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print_error("Sample entry has not been specified!", "Line", line)
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@ -94,23 +143,55 @@ def check_samplesheet(file_in, file_out):
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if fastq:
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if fastq.find(" ") != -1:
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print_error("FastQ file contains spaces!", "Line", line)
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if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
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if not fastq.endswith(FQ_EXTENSIONS):
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print_error(
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"FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
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f"FastQ file does not have extension {' or '.join(list(FQ_EXTENSIONS))} !",
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"Line",
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line,
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)
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if fasta:
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if fasta.find(" ") != -1:
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print_error("FastA file contains spaces!", "Line", line)
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if not fasta.endswith(FA_EXTENSIONS):
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print_error(
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f"FastA file does not have extension {' or '.join(list(FA_EXTENSIONS))}!",
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"Line",
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line,
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)
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sample_info = []
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# Check run_accession
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if not run_accession:
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print_error("Run accession has not been specified!", "Line", line)
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else:
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sample_info.append(run_accession)
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# Check instrument_platform
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if not instrument_platform:
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print_error("Instrument platform has not been specified!", "Line", line)
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else:
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if instrument_platform not in INSTRUMENT_PLATFORMS:
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print_error(
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f"Instrument platform {instrument_platform} is not supported!",
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f"List of supported platforms {', '.join(INSTRUMENT_PLATFORMS)}",
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"Line",
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line,
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)
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sample_info.append(instrument_platform)
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## Auto-detect paired-end/single-end
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sample_info = [] ## [single_end, fastq_1, fastq_2]
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if sample and fastq_1 and fastq_2: ## Paired-end short reads
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sample_info = ["0", fastq_1, fastq_2]
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sample_info.extend(["0", fastq_1, fastq_2, fasta])
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elif sample and fastq_1 and not fastq_2: ## Single-end short reads
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sample_info = ["1", fastq_1, fastq_2]
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif (
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sample and fasta and not fastq_1 and not fastq_2
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): ## Single-end long reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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else:
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print_error("Invalid combination of columns provided!", "Line", line)
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## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] }
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## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 , fasta, run_accession, instrument_platform] }
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if sample not in sample_mapping_dict:
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sample_mapping_dict[sample] = [sample_info]
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else:
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@ -120,19 +201,36 @@ def check_samplesheet(file_in, file_out):
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sample_mapping_dict[sample].append(sample_info)
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## Write validated samplesheet with appropriate columns
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HEADER_OUT = [
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"sample",
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"run_accession",
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"instrument_platform",
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"single_end",
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"fastq_1",
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"fastq_2",
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"fasta",
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]
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if len(sample_mapping_dict) > 0:
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out_dir = os.path.dirname(file_out)
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make_dir(out_dir)
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with open(file_out, "w") as fout:
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fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
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fout.write(",".join(HEADER_OUT) + "\n")
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for sample in sorted(sample_mapping_dict.keys()):
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## Check that multiple runs of the same sample are of the same datatype
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if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
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print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample))
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if not all(
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x[0] == sample_mapping_dict[sample][0][0]
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for x in sample_mapping_dict[sample]
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):
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print_error(
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"Multiple runs of a sample must be of the same datatype!",
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"Sample: {}".format(sample),
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)
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for idx, val in enumerate(sample_mapping_dict[sample]):
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fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n")
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fout.write(
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",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n"
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)
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else:
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print_error("No entries to process!", "Samplesheet: {}".format(file_in))
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