-
Notifications
You must be signed in to change notification settings - Fork 4
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #92 from sanger-tol/dev
Release 0.3
- Loading branch information
Showing
50 changed files
with
1,005 additions
and
168 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,252 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
|
|
||
| """Provide a command line tool to validate and transform tabular samplesheets.""" | ||
|
|
||
|
|
||
| import argparse | ||
| import csv | ||
| import logging | ||
| import sys | ||
| from collections import Counter | ||
| from pathlib import Path | ||
|
|
||
| logger = logging.getLogger() | ||
|
|
||
|
|
||
| class RowChecker: | ||
| """ | ||
| Define a service that can validate and transform each given row. | ||
| Attributes: | ||
| modified (list): A list of dicts, where each dict corresponds to a previously | ||
| validated and transformed row. The order of rows is maintained. | ||
| """ | ||
|
|
||
| VALID_FORMATS = (".fastq.gz",) | ||
|
|
||
| def __init__( | ||
| self, | ||
| accession_col="run_accession", | ||
| model_col="instrument_model", | ||
| platform_col="instrument_platform", | ||
| library_col="library_strategy", | ||
| file1_col="fastq_1", | ||
| file2_col="fastq_2", | ||
| **kwargs, | ||
| ): | ||
| """ | ||
| Initialize the row checker with the expected column names. | ||
| Args: | ||
| accession_col (str): The name of the column that contains the accession name | ||
| (default "run_accession"). | ||
| model_col (str): The name of the column that contains the model name | ||
| of the instrument (default "instrument_model"). | ||
| platform_col (str): The name of the column that contains the platform name | ||
| of the instrument (default "instrument_platform"). | ||
| library_col (str): The name of the column that contains the strategy of the | ||
| preparation of the library (default "library_strategy"). | ||
| file2_col (str): The name of the column that contains the second file path | ||
| for the paired-end read data (default "fastq_2"). | ||
| """ | ||
| super().__init__(**kwargs) | ||
| self._accession_col = accession_col | ||
| self._model_col = model_col | ||
| self._platform_col = platform_col | ||
| self._library_col = library_col | ||
| self._file1_col = file1_col | ||
| self._file2_col = file2_col | ||
| self._seen = set() | ||
| self.modified = [] | ||
|
|
||
| def validate_and_transform(self, row): | ||
| """ | ||
| Perform all validations on the given row. | ||
| Args: | ||
| row (dict): A mapping from column headers (keys) to elements of that row | ||
| (values). | ||
| """ | ||
| self._validate_accession(row) | ||
| self._validate_file(row) | ||
| self._seen.add((row[self._accession_col], row[self._file1_col])) | ||
| self.modified.append(row) | ||
|
|
||
| def _validate_accession(self, row): | ||
| """Assert that the run accession name exists.""" | ||
| if len(row[self._accession_col]) <= 0: | ||
| raise AssertionError("Run accession is required.") | ||
|
|
||
| def _validate_file(self, row): | ||
| """Assert that the datafile is non-empty and has the right format.""" | ||
| if len(row[self._file1_col]) <= 0: | ||
| raise AssertionError("Data file is required.") | ||
| self._validate_data_format(row[self._file1_col]) | ||
| if row[self._file2_col]: | ||
| self._validate_data_format(row[self._file2_col]) | ||
|
|
||
| def _validate_data_format(self, filename): | ||
| """Assert that a given filename has one of the expected FASTQ extensions.""" | ||
| if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): | ||
| raise AssertionError( | ||
| f"The data file has an unrecognized extension: {filename}\n" | ||
| f"It should be one of: {', '.join(self.VALID_FORMATS)}" | ||
| ) | ||
|
|
||
| def validate_unique_accessions(self): | ||
| """ | ||
| Assert that the combination of accession name and aligned filename is unique. | ||
| In addition to the validation, also rename all accessions to have a suffix of _T{n}, where n is the | ||
| number of times the same accession exist, but with different FASTQ files, e.g., multiple runs per experiment. | ||
| """ | ||
| if len(self._seen) != len(self.modified): | ||
| raise AssertionError("The pair of accession and file name must be unique.") | ||
| seen = Counter() | ||
| for row in self.modified: | ||
| accession = row[self._accession_col] | ||
| seen[accession] += 1 | ||
| row[self._accession_col] = f"{accession}_T{seen[accession]}" | ||
|
|
||
|
|
||
| def read_head(handle, num_lines=10): | ||
| """Read the specified number of lines from the current position in the file.""" | ||
| lines = [] | ||
| for idx, line in enumerate(handle): | ||
| if idx == num_lines: | ||
| break | ||
| lines.append(line) | ||
| return "".join(lines) | ||
|
|
||
|
|
||
| def sniff_format(handle): | ||
| """ | ||
| Detect the tabular format. | ||
| Args: | ||
| handle (text file): A handle to a `text file`_ object. The read position is | ||
| expected to be at the beginning (index 0). | ||
| Returns: | ||
| csv.Dialect: The detected tabular format. | ||
| .. _text file: | ||
| https://docs.python.org/3/glossary.html#term-text-file | ||
| """ | ||
| peek = read_head(handle) | ||
| handle.seek(0) | ||
| sniffer = csv.Sniffer() | ||
| dialect = sniffer.sniff(peek) | ||
| return dialect | ||
|
|
||
|
|
||
| def check_samplesheet(file_in, file_out): | ||
| """ | ||
| Check that the tabular samplesheet has the structure expected by sanger-tol pipelines. | ||
| Validate the general shape of the table, expected columns, and each row. Also add | ||
| Args: | ||
| file_in (pathlib.Path): The given tabular samplesheet. The format can be either | ||
| CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. | ||
| file_out (pathlib.Path): Where the validated and transformed samplesheet should | ||
| be created; always in CSV format. | ||
| Example: | ||
| This function checks that the samplesheet follows the following structure, | ||
| see also the `blobtoolkit samplesheet`_:: | ||
| sample,datatype,datafile | ||
| sample1,hic,/path/to/file1.cram | ||
| sample1,pacbio,/path/to/file2.cram | ||
| sample1,ont,/path/to/file3.cram | ||
| .. _blobtoolkit samplesheet: | ||
| https://raw.githubusercontent.com/sanger-tol/blobtoolkit/main/assets/test/samplesheet.csv | ||
| """ | ||
| required_columns = { | ||
| "run_accession", | ||
| "instrument_model", | ||
| "instrument_platform", | ||
| "library_strategy", | ||
| "fastq_1", | ||
| "fastq_2", | ||
| } | ||
| # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. | ||
| with file_in.open(newline="") as in_handle: | ||
| reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) | ||
| # Validate the existence of the expected header columns. | ||
| if not required_columns.issubset(reader.fieldnames): | ||
| req_cols = ", ".join(required_columns) | ||
| logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") | ||
| sys.exit(1) | ||
| # Validate each row. | ||
| checker = RowChecker() | ||
| for i, row in enumerate(reader): | ||
| try: | ||
| checker.validate_and_transform(row) | ||
| except AssertionError as error: | ||
| logger.critical(f"{str(error)} On line {i + 2}.") | ||
| sys.exit(1) | ||
| checker.validate_unique_accessions() | ||
| header = list(reader.fieldnames) | ||
| # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. | ||
| with file_out.open(mode="w", newline="") as out_handle: | ||
| writer = csv.DictWriter(out_handle, header, delimiter=",") | ||
| writer.writeheader() | ||
| for row in checker.modified: | ||
| writer.writerow(row) | ||
|
|
||
|
|
||
| def parse_args(argv=None): | ||
| """Define and immediately parse command line arguments.""" | ||
| parser = argparse.ArgumentParser( | ||
| description="Validate and transform a tabular samplesheet.", | ||
| epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", | ||
| ) | ||
| parser.add_argument( | ||
| "file_in", | ||
| metavar="FILE_IN", | ||
| type=Path, | ||
| help="Tabular input samplesheet in CSV or TSV format.", | ||
| ) | ||
| parser.add_argument( | ||
| "file_out", | ||
| metavar="FILE_OUT", | ||
| type=Path, | ||
| help="Transformed output samplesheet in CSV format.", | ||
| ) | ||
| parser.add_argument( | ||
| "-l", | ||
| "--log-level", | ||
| help="The desired log level (default WARNING).", | ||
| choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), | ||
| default="WARNING", | ||
| ) | ||
| parser.add_argument( | ||
| "-v", | ||
| "--version", | ||
| action="version", | ||
| version="%(prog)s 1.0.0", | ||
| ) | ||
| return parser.parse_args(argv) | ||
|
|
||
|
|
||
| def main(argv=None): | ||
| """Coordinate argument parsing and program execution.""" | ||
| args = parse_args(argv) | ||
| logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") | ||
| if not args.file_in.is_file(): | ||
| logger.error(f"The given input file {args.file_in} was not found!") | ||
| sys.exit(2) | ||
| args.file_out.parent.mkdir(parents=True, exist_ok=True) | ||
| check_samplesheet(args.file_in, args.file_out) | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| sys.exit(main()) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -27,6 +27,8 @@ class RowChecker: | |
| VALID_FORMATS = ( | ||
| ".cram", | ||
| ".bam", | ||
| ".fastq", | ||
| ".fastq.gz", | ||
| ) | ||
|
|
||
| VALID_DATATYPES = ( | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.