FRMatcher

FRMatcher categorizes a list of presumably FASTQ files into R1 (forward reads) and R2 (reverse reads) pairs using customizable pattern matching.

Installation

Clone the repository:

git clone https://github.com/odinokov/frmatcher.git
cd frmatcher

Activate the virtual environment:

poetry shell

Build the package:

poetry build

Install the package locally:

poetry install

Usage

from frmatcher import FastqFileNameChecker

filenames = [
    "sample_1_L001.fastq.gz",
    "sample_2_L001.fastq.gz",
    "sample_1_L002.fastq.gz",
    "sample_2_L002.fastq.gz",
]

checker = FastqFileNameChecker(filenames,
                              length_check=False,
                              verbose=False)

# checker = FastqFileNameChecker(filenames,
#                                length_check=True,
#                                verbose=True,
#                                config_path=None)
# checker.patterns = {
#     'r1': ["_1", "_R1"],
#     'r2': ["_2", "_R2"],
#     'ignore': ["^i_", "^I_", "_i\\d+", "_I\\d+"]
# }

categorized_files = checker.categorize_fastq_files()

print(categorized_files)

# {'R1': ['sample_1_L001.fastq.gz', 'sample_1_L002.fastq.gz'],
# 'R2': ['sample_2_L001.fastq.gz', 'sample_2_L002.fastq.gz'],
# 'ignored': []}

License

MIT License. See the LICENSE file for details.