python samplesheet _check changes

    """

    This function checks that the samplesheet follows the following structure:

    group,replicate,control_group,fastq_1,fastq_2

    WT,1,1,WT_LIB1_REP1_1.fastq.gz,WT_LIB1_REP1_2.fastq.gz

    WT,1,1,WT_LIB2_REP1_1.fastq.gz,WT_LIB2_REP1_2.fastq.gz

    WT,2,1,WT_LIB1_REP2_1.fastq.gz,WT_LIB1_REP2_2.fastq.gz

    KO,1,2,KO_LIB1_REP1_1.fastq.gz,KO_LIB1_REP1_2.fastq.gz

    IGG,1,1,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz

    IGG,2,2,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz

    group,replicate,fastq_1,fastq_2,control

    WT,1,WT_LIB1_REP1_1.fastq.gz,WT_LIB1_REP1_2.fastq.gz,IGG_group1

    WT,1,WT_LIB2_REP1_1.fastq.gz,WT_LIB2_REP1_2.fastq.gz,IGG_group1

    WT,2,WT_LIB1_REP2_1.fastq.gz,WT_LIB1_REP2_2.fastq.gz,IGG_group1

    KO,1,KO_LIB1_REP1_1.fastq.gz,KO_LIB1_REP1_2.fastq.gz,IGG_group1

    IGG_group1,1,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz, 

    IGG_group1,2,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz, 

    """

    igg_present = False

    num_fastq_list     = []

    sample_names_list  = []

    control_names_list = []

    sample_run_dict = {}

    with open(file_in, "r") as fin:

        ## Check header

        MIN_COLS = 3

        HEADER = ["group", "replicate", "control_group", "fastq_1", "fastq_2"]

        HEADER = ["group", "replicate", "fastq_1", "fastq_2", "control"]

        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)))

        for line in fin:

            lspl = [x.strip().strip('"') for x in line.strip().split(",")]

            ## Set control_present to true if the control column is not empty

            if not igg_present:

                if 'igg' in lspl:

                if lspl[4] != "":

                    igg_present = True 

            ## Check valid number of columns per row

            if len(lspl) < len(HEADER):

            if len(lspl) != 5:

                print_error(

                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),

                    "Invalid number of columns (should be {})!".format(len(HEADER)),

                    "Line",

                    line,

                )

            ## Check valid number of populated columns per row

            num_cols = len([x for x in lspl if x])

            if num_cols < MIN_COLS:

                print_error(

                )

            ## Check sample name entries

            sample, replicate, control_group, fastq_1, fastq_2 = lspl[: len(HEADER)]

            sample, replicate, fastq_1, fastq_2, control = lspl[: len(HEADER)]

            if sample:

                if sample.find(" ") != -1:

                    print_error("Group entry contains spaces!", "Line", line)

            else:

                print_error("Group entry has not been specified!", "Line", line)

            if control:

                if control.find(" ") != -1:

                    print_error("Control entry contains spaces!", "Line", line)

            ## Check control sample name is not equal to sample name entry

            if sample == control:

                print_error("Control entry and sample entry must be different!", "Line", line)

            ## Check replicate entry is integer

            if not replicate.isdigit():

                print_error("Replicate id not an integer!", "Line", line)

                            "Line",

                            line,

                        )

            num_fastq = len([fastq for fastq in [fastq_1, fastq_2] if fastq])

            num_fastq_list.append(num_fastq)

            ## Auto-detect paired-end/single-end

            sample_info = []

            if sample and fastq_1 and fastq_2:  ## Paired-end short reads

                sample_info = [sample, str(replicate), control_group, "0", fastq_1, fastq_2]

                sample_info = [sample, str(replicate), control, "0", fastq_1, fastq_2]

            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads

                sample_info = [sample, str(replicate), control_group, "1", fastq_1, fastq_2]

                sample_info = [sample, str(replicate), control, "1", fastq_1, fastq_2]

            else:

                print_error("Invalid combination of columns provided!", "Line", line)

            ## Create sample mapping dictionary = {sample: {replicate : [ single_end, fastq_1, fastq_2 ]}}

                else:

                    sample_run_dict[sample][replicate].append(sample_info)

            ## Store unique group names

            if sample not in sample_names_list:

                sample_names_list.append(sample)

            ## Store unique control names

            if control not in control_names_list:

                control_names_list.append(control)

    ## Check data is either paired-end/single-end and not both

    if min(num_fastq_list) != max(num_fastq_list):

        print_error("Mixture of paired-end and single-end reads!")

        sys.exit(1)

    ## Check control group exists

    for ctrl in control_names_list:

        if ctrl != "" and ctrl not in sample_names_list:

            CTRL = ctrl

            print_error("Each control entry must match at least one group entry! Unmatched control entry: {}.".format(CTRL))

            sys.exit(1)

    ## Check igg_control parameter is consistent with input groups

    if (igg_control == 'true' and not igg_present):

        print("ERROR: No 'igg' group was found in " + str(file_in) + " If you are not supplying an IgG control, please specify --igg_control 'false' on command line.")

        print("ERROR: Parameter --igg_control was set to false, but an 'igg' group was found in " + str(file_in) + ".")

        sys.exit(1)

    ## Check control groups have unique ids that are the same as their replicate ids

    control_group_ids = []

    if igg_present:

        for key, data in sample_run_dict["igg"].items():

            for tech_rep in data:

                if tech_rep[2] not in control_group_ids:

                    control_group_ids.append(tech_rep[2])

                if(tech_rep[2] != str(key)):

                    print("ERROR: IgG groups must have a control id equal to the replicate id")

                    sys.exit(1)

    ## Write validated samplesheet with appropriate columns

    if len(sample_run_dict) > 0:

        out_dir = os.path.dirname(file_out)

        make_dir(out_dir)

        with open(file_out, "w") as fout:

            fout.write(",".join(["id", "group", "replicate", "control_group", "single_end", "fastq_1", "fastq_2"]) + "\n")

            fout.write(",".join(["id", "group", "replicate", "control", "single_end", "fastq_1", "fastq_2"]) + "\n")

            for sample in sorted(sample_run_dict.keys()):

                ## Check that replicate ids are in format 1..<NUM_REPS>

                    )

                for replicate in sorted(sample_run_dict[sample].keys()):

                    ## Check control group exists

                    if igg_present:

                        for tech_rep in sample_run_dict[sample][replicate]:

                            if tech_rep[2] not in control_group_ids:

                                print_error(

                                    "Control group does not exist",

                                    tech_rep[2]

                                )

                    ## Check tech reps have same control group id

                    check_group = sample_run_dict[sample][replicate][0][2]

                    for tech_rep in sample_run_dict[sample][replicate]: