check_samplesheet.py

#!/usr/bin/env python

import os
import sys
import errno
import argparse


def parse_args(args=None):
    Description = "Reformat nf-core/viralrecon samplesheet file and check its contents."
    Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"

    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
    parser.add_argument("FILE_IN", help="Input samplesheet file.")
    parser.add_argument("FILE_OUT", help="Output file.")
    parser.add_argument(
        "-pl",
        "--platform",
        type=str,
        dest="PLATFORM",
        default="illumina",
        help="Sequencing platform for input data. Accepted values = 'illumina' or 'nanopore'  (default: 'illumina').",
    )
    return parser.parse_args(args)


def make_dir(path):
    if len(path) > 0:
        try:
            os.makedirs(path)
        except OSError as exception:
            if exception.errno != errno.EEXIST:
                raise exception


def print_error(error, context="Line", context_str=""):
    error_str = "ERROR: Please check samplesheet -> {}".format(error)
    if context != "" and context_str != "":
        error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
            error, context.strip(), context_str.strip()
        )
    print(error_str)
    sys.exit(1)


def check_illumina_samplesheet(file_in, file_out):
    """
    This function checks that the samplesheet follows the following structure:

    sample,fastq_1,fastq_2
    SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
    SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
    SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,

    For an example see:
    https://github.com/nf-core/test-datasets/blob/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
    """

    sample_mapping_dict = {}
    with open(file_in, "r") as fin:

        ## Check header
        MIN_COLS = 2
        HEADER = ["sample", "fastq_1", "fastq_2"]
        header = [x.strip('"') for x in fin.readline().strip().split(",")]
        if header[: len(HEADER)] != HEADER:
            print(
                "ERROR: Please check samplesheet header -> {} != {}".format(
                    ",".join(header), ",".join(HEADER)
                )
            )
            sys.exit(1)

        ## Check sample entries
        for line in fin:
            lspl = [x.strip().strip('"') for x in line.strip().split(",")]

            # Check valid number of columns per row
            if len(lspl) < len(HEADER):
                print_error(
                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
                    "Line",
                    line,
                )
            num_cols = len([x for x in lspl if x])
            if num_cols < MIN_COLS:
                print_error(
                    "Invalid number of populated columns (minimum = {})!".format(
                        MIN_COLS
                    ),
                    "Line",
                    line,
                )

            ## Check sample name entries
            sample, fastq_1, fastq_2 = lspl[: len(HEADER)]
            if sample.find(" ") != -1:
                print(
                    f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
                )
                sample = sample.replace(" ", "_")
            if sample.find("-") != -1:
                print(
                    f"WARNING: Dashes have been replaced by underscores for sample: {sample}"
                )
                sample = sample.replace("-", "_")
            if not sample:
                print_error("Sample entry has not been specified!", "Line", line)

            ## Check FastQ file extension
            for fastq in [fastq_1, fastq_2]:
                if fastq:
                    if fastq.find(" ") != -1:
                        print_error("FastQ file contains spaces!", "Line", line)
                    if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
                        print_error(
                            "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
                            "Line",
                            line,
                        )

            ## Auto-detect paired-end/single-end
            sample_info = []  ## [single_end, fastq_1, fastq_2]
            if sample and fastq_1 and fastq_2:  ## Paired-end short reads
                sample_info = ["0", fastq_1, fastq_2]
            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
                sample_info = ["1", fastq_1, fastq_2]
            else:
                print_error("Invalid combination of columns provided!", "Line", line)

            ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] }
            if sample not in sample_mapping_dict:
                sample_mapping_dict[sample] = [sample_info]
            else:
                if sample_info in sample_mapping_dict[sample]:
                    print_error("Samplesheet contains duplicate rows!", "Line", line)
                else:
                    sample_mapping_dict[sample].append(sample_info)

    ## Write validated samplesheet with appropriate columns
    if len(sample_mapping_dict) > 0:
        out_dir = os.path.dirname(file_out)
        make_dir(out_dir)
        with open(file_out, "w") as fout:
            fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
            for sample in sorted(sample_mapping_dict.keys()):

                ## Check that multiple runs of the same sample are of the same datatype
                if not all(
                    x[0] == sample_mapping_dict[sample][0][0]
                    for x in sample_mapping_dict[sample]
                ):
                    print_error(
                        "Multiple runs of a sample must be of the same datatype!",
                        "Sample: {}".format(sample),
                    )

                for idx, val in enumerate(sample_mapping_dict[sample]):
                    fout.write(
                        ",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n"
                    )
    else:
        print_error("No entries to process!", "Samplesheet: {}".format(file_in))


def check_nanopore_samplesheet(file_in, file_out):
    """
    This function checks that the samplesheet follows the following structure:

    sample,barcode
    SAMPLE_N,1
    SAMPLE_X,2
    SAMPLE_Z,3

    For an example see:
    https://github.com/nf-core/test-datasets/blob/viralrecon/samplesheet/samplesheet_test_nanopore.csv
    """

    sample_mapping_dict = {}
    with open(file_in, "r") as fin:

        ## Check header
        MIN_COLS = 2
        HEADER = ["sample", "barcode"]
        header = [x.strip('"') for x in fin.readline().strip().split(",")]
        if header[: len(HEADER)] != HEADER:
            print(
                "ERROR: Please check samplesheet header -> {} != {}".format(
                    ",".join(header), ",".join(HEADER)
                )
            )
            sys.exit(1)

        ## Check sample entries
        for line in fin:
            lspl = [x.strip().strip('"') for x in line.strip().split(",")]

            # Check valid number of columns per row
            if len(lspl) < len(HEADER):
                print_error(
                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
                    "Line",
                    line,
                )
            num_cols = len([x for x in lspl if x])
            if num_cols < MIN_COLS:
                print_error(
                    "Invalid number of populated columns (minimum = {})!".format(
                        MIN_COLS
                    ),
                    "Line",
                    line,
                )

            ## Check sample entry
            sample, barcode = lspl[: len(HEADER)]
            if sample.find(" ") != -1:
                print(
                    f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
                )
                sample = sample.replace(" ", "_")
            if sample.find("-") != -1:
                print(
                    f"WARNING: Dashes have been replaced by underscores for sample: {sample}"
                )
                sample = sample.replace("-", "_")
            if not sample:
                print_error("Sample entry has not been specified!", "Line", line)

            ## Check barcode entry
            if barcode:
                if not barcode.isdigit():
                    print_error("Barcode entry is not an integer!", "Line", line)
                else:
                    barcode = "barcode%s" % (barcode.zfill(2))

            ## Create sample mapping dictionary = { sample: barcode }
            if barcode in sample_mapping_dict.values():
                print_error(
                    "Samplesheet contains duplicate entries in the 'barcode' column!",
                    "Line",
                    line,
                )
            if sample not in sample_mapping_dict:
                sample_mapping_dict[sample] = barcode
            else:
                print_error(
                    "Samplesheet contains duplicate entries in the 'sample' column!",
                    "Line",
                    line,
                )

    ## Write validated samplesheet with appropriate columns
    if len(sample_mapping_dict) > 0:
        out_dir = os.path.dirname(file_out)
        make_dir(out_dir)
        with open(file_out, "w") as fout:
            fout.write(",".join(["sample", "barcode"]) + "\n")
            for sample in sorted(sample_mapping_dict.keys()):
                fout.write(",".join([sample, sample_mapping_dict[sample]]) + "\n")
    else:
        print_error("No entries to process!", "Samplesheet: {}".format(file_in))


def main(args=None):
    args = parse_args(args)

    if args.PLATFORM == "illumina":
        check_illumina_samplesheet(args.FILE_IN, args.FILE_OUT)
    elif args.PLATFORM == "nanopore":
        check_nanopore_samplesheet(args.FILE_IN, args.FILE_OUT)
    else:
        print(
            "Unrecognised option passed to --platform: {}. Accepted values = 'illumina' or 'nanopore'".format(
                args.PLATFORM
            )
        )
        sys.exit(1)


if __name__ == "__main__":
    sys.exit(main())