19136367672

Committed 06 Nov 2025 12:56PM UTC coverage: 68.835% (-0.4%) from 69.186%

Build # 19136367672

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #875 from cokelaer/dev

update HTML variant calling + others

Run Details

157 of 332 new or added lines in 14 files covered. (47.29%)

5 existing lines in 3 files now uncovered.

14551 of 21139 relevant lines covered (68.83%)

1.38 hits per line

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55.0

/sequana/scripts/main/fastq_split.py

# sequana/cli/fastq_split.py
import rich_click as click

from sequana import logger
from sequana.fastq_splitter import FastqSplitter


@click.command(name="fastq-split")
@click.argument("input_fastq", type=click.Path(exists=True))
@click.option("--by-size", type=int, help="Split file into chunks of N reads each.")
@click.option("--by-part", type=int, help="Split file into N equal parts.")
@click.option(
    "--pattern",
    default="output.#.fastq.gz",
    show_default=True,
    help="Output filename pattern (use # as placeholder for chunk number).",
)
@click.option("--gzip", "gzip_output", is_flag=True, help="Compress output with gzip.")
@click.option(
    "--buffer-size",
    type=int,
    default=10000,
    show_default=True,
    help="Number of reads to buffer before writing to disk.",
)
def fastq_split(input_fastq, by_size, by_part, pattern, gzip_output, buffer_size):
    """
    Split a FASTQ file into smaller parts (by number of reads or by number of parts).

    Examples:

        sequana fastq-split reads.fastq --by-size 1000000 --pattern chunk.#.fastq.gz

        sequana fastq-split reads.fastq.gz --by-part 10 --pattern sample.#.fastq.gz
    """
    if (by_size and by_part) or not (by_size or by_part):
        raise click.UsageError("Use either --by-size or --by-part, not both.")

    splitter = FastqSplitter(input_fastq)

    if by_size:
        logger.info(f"Splitting {input_fastq} into chunks of {by_size} reads each.")
        splitter.by_size(by_size, pattern, gzip_output, buffer_size)
    else:
        logger.info(f"Splitting {input_fastq} into {by_part} equal parts.")
        splitter.by_part(by_part, pattern, gzip_output, buffer_size)

    logger.info("Splitting completed successfully.")

1	# sequana/cli/fastq_split.py
2	import rich_click as click	3✔
3
4	from sequana import logger	3✔
5	from sequana.fastq_splitter import FastqSplitter	3✔
6
7
8	@click.command(name="fastq-split")	3✔
9	@click.argument("input_fastq", type=click.Path(exists=True))	3✔
10	@click.option("--by-size", type=int, help="Split file into chunks of N reads each.")	3✔
11	@click.option("--by-part", type=int, help="Split file into N equal parts.")	3✔
12	@click.option(	3✔
13	"--pattern",
14	default="output.#.fastq.gz",
15	show_default=True,
16	help="Output filename pattern (use # as placeholder for chunk number).",
17	)
18	@click.option("--gzip", "gzip_output", is_flag=True, help="Compress output with gzip.")	3✔
19	@click.option(	3✔
20	"--buffer-size",
21	type=int,
22	default=10000,
23	show_default=True,
24	help="Number of reads to buffer before writing to disk.",
25	)
26	def fastq_split(input_fastq, by_size, by_part, pattern, gzip_output, buffer_size):	3✔
27	"""
28	Split a FASTQ file into smaller parts (by number of reads or by number of parts).
29
30	Examples:
31
32	sequana fastq-split reads.fastq --by-size 1000000 --pattern chunk.#.fastq.gz
33
34	sequana fastq-split reads.fastq.gz --by-part 10 --pattern sample.#.fastq.gz
35	"""
NEW 36	if (by_size and by_part) or not (by_size or by_part):	×
NEW 37	raise click.UsageError("Use either --by-size or --by-part, not both.")	×
38
NEW 39	splitter = FastqSplitter(input_fastq)	×
40
NEW 41	if by_size:	×
NEW 42	logger.info(f"Splitting {input_fastq} into chunks of {by_size} reads each.")	×
NEW 43	splitter.by_size(by_size, pattern, gzip_output, buffer_size)	×
44	else:
NEW 45	logger.info(f"Splitting {input_fastq} into {by_part} equal parts.")	×
NEW 46	splitter.by_part(by_part, pattern, gzip_output, buffer_size)	×
47
NEW 48	logger.info("Splitting completed successfully.")	×

sequana / sequana / 19136367672

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