From 4dd234db93320d8b10853e01f2865bf5b5199f9f Mon Sep 17 00:00:00 2001 From: Gesina Phillips Date: Wed, 23 Oct 2024 14:30:55 -0400 Subject: [PATCH] fixing set_num regex --- src/ingest_validation_tests/fastq_validator_logic.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ingest_validation_tests/fastq_validator_logic.py b/src/ingest_validation_tests/fastq_validator_logic.py index bb34106..f021782 100644 --- a/src/ingest_validation_tests/fastq_validator_logic.py +++ b/src/ingest_validation_tests/fastq_validator_logic.py @@ -29,14 +29,14 @@ def get_prefix_read_type_and_set(filename: str) -> Optional[filename_pattern]: """ if not bool(fastq_utils.FASTQ_PATTERN.fullmatch(filename)): return - # looking for fastq filenames matching pattern __[I1,I2,R1,R2,R3]_ + # looking for fastq filenames matching pattern __[I1,I2,R1,R2,R3]_ pattern = re.compile( - r"(?P.*(?:L\d+)(?=[_](?:(?P(?:R|read)(?=[123]_)|I(?=[12]_)))))" + r"(?P.*(?:L\d+)(?=[_](?:(?P(?:R|read)(?=[123])|I(?=[12]))(?:\d?_)(?P\d+))))" ) groups = pattern.match(filename) - if groups and all(x in groups.groupdict().keys() for x in ["prefix", "read_type", "set"]): + if groups and all(x in groups.groupdict().keys() for x in ["prefix", "read_type", "set_num"]): return filename_pattern( - groups.group("prefix"), groups.group("read_type"), groups.group("set") + groups.group("prefix"), groups.group("read_type"), groups.group("set_num") )