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add more columns to samplesheet

This commit is contained in:
maxibor 2022-02-18 11:53:13 +01:00
parent 12e7b428f2
commit f867c057a4

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