mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-26 03:09:56 +00:00
117 lines
4.3 KiB
Python
117 lines
4.3 KiB
Python
#!/usr/bin/env python
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import argparse
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import csv
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import logging
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import sys
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from enum import Enum
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from typing import List, NoReturn, Optional
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class ColumnNames(str, Enum):
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SAMPLE = "sample"
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FASTQ_1 = "fastq_1"
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FASTQ_2 = "fastq_2"
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FASTA = "fasta"
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SINGLE_END = "single_end"
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def parse_args(args: Optional[List[str]] = None) -> argparse.Namespace:
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"""
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Reformatting is based on detecting whether the reads are paired or single end.
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Script appends appropriate column to samplesheet.csv file.
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"""
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parser = argparse.ArgumentParser(
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description="Reformat nf-core/taxprofiler samplesheet file.",
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epilog="Example usage: python detect_reads.py <FILE_IN> <FILE_OUT>",
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)
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parser.add_argument("FILE_IN", help="Input samplesheet file.")
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parser.add_argument("FILE_OUT", help="Output file.")
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return parser.parse_args(args)
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class ReadsModifier:
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def __init__(self):
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self.headers = None
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self.sample_index = None
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self.fastq_1_index = None
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self.fastq_2_index = None
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self.fasta_index = None
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def detect_reads_and_reformat(self, input_file_path: str, output_file_path: str) -> NoReturn:
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new_file_rows = []
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with open(input_file_path, "r", newline="") as input_file:
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csv_reader = csv.DictReader(input_file, delimiter=",")
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self.headers = csv_reader.fieldnames
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self.headers.append("single_end")
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for samplesheet_row in csv_reader:
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if self._is_paired_end_short_read(samplesheet_row):
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samplesheet_row[ColumnNames.SINGLE_END] = "0"
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new_file_rows.append(samplesheet_row.values())
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elif self._is_single_end_short_long_read(samplesheet_row):
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samplesheet_row[ColumnNames.SINGLE_END] = "1"
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new_file_rows.append(samplesheet_row.values())
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elif self._is_single_end_long_read(samplesheet_row):
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samplesheet_row[ColumnNames.SINGLE_END] = "1"
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new_file_rows.append(samplesheet_row.values())
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elif self._is_error_row(samplesheet_row):
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logging.error(
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"FastQ and FastA files cannot be specified together in the same library!",
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"Line",
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",".join(samplesheet_row.values()),
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)
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else:
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logging.error(
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"Invalid combination of columns provided!", "Line", ",".join(samplesheet_row.values())
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)
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ReadsModifier.save_reformatted_samplesheet([self.headers] + new_file_rows, output_file_path)
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def _get_row_values(self, samplesheet_row: dict):
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"""
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This method extracts data from the columns for given row of samplesheet table.
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"""
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return (
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samplesheet_row.get(ColumnNames.SAMPLE),
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samplesheet_row.get(ColumnNames.FASTQ_1),
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samplesheet_row.get(ColumnNames.FASTQ_2),
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samplesheet_row.get(ColumnNames.FASTA),
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)
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def _is_paired_end_short_read(self, samplesheet_row: dict) -> bool:
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sample, fastq_1, fastq_2, _ = self._get_row_values(samplesheet_row)
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return sample and fastq_1 and fastq_2
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def _is_single_end_short_long_read(self, samplesheet_row: dict) -> bool:
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sample, fastq_1, fastq_2, _ = self._get_row_values(samplesheet_row)
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return sample and fastq_1 and not fastq_2
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def _is_single_end_long_read(self, samplesheet_row: dict) -> bool:
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sample, fastq_1, fastq_2, fasta = self._get_row_values(samplesheet_row)
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return sample and fasta and not fastq_1 and not fastq_2
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def _is_error_row(self, samplesheet_row: dict) -> bool:
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sample, fastq_1, fastq_2, fasta = self._get_row_values(samplesheet_row)
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return fasta and (fastq_1 or fastq_2)
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@classmethod
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def save_reformatted_samplesheet(cls, new_file_rows: List[List], output_file_path: str) -> NoReturn:
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"""
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Write new samplesheet.
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"""
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with open(output_file_path, "w") as output_file:
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csv.writer(output_file).writerows(new_file_rows)
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def main(args=None):
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args = parse_args(args)
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ReadsModifier().detect_reads_and_reformat(args.FILE_IN, args.FILE_OUT)
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if __name__ == "__main__":
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sys.exit(main())
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