28578229798

Committed 02 Jul 2026 09:01AM UTC coverage: 70.046% (-0.6%) from 70.652%

Build # 28578229798

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #907 from cokelaer/main

add non b-DNA modules

Coverage Stats

1213 of 1758 new or added lines in 30 files covered. (69.0%)

324 existing lines in 4 files now uncovered.

16491 of 23543 relevant lines covered (70.05%)

2.1 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

66.67

/sequana/scripts/main/samplesheet.py

#  This file is part of Sequana software
#
#  Copyright (c) 2016-2020 - Sequana Development Team
#
#  Distributed under the terms of the 3-clause BSD license.
#  The full license is in the LICENSE file, distributed with this software.
#
#  website: https://github.com/sequana/sequana
#  documentation: http://sequana.readthedocs.io
#
##############################################################################
import colorlog
import rich_click as click

from sequana.iem import SampleSheetFactory
from sequana.scripts.utils import CONTEXT_SETTINGS

logger = colorlog.getLogger(__name__)


@click.command(context_settings=CONTEXT_SETTINGS)
@click.argument("name", type=click.STRING)
@click.option("--check", is_flag=True, help="report validity of the input file")
@click.option("--full-check", is_flag=True, help="report complete report of all checks")
@click.option(
    "--extract-adapters",
    is_flag=True,
    help="extract adapters from the settings section and save them into a fasta file",
)
@click.option("--quick-fix", is_flag=True)
@click.option("--output", default=None)
def samplesheet(**kwargs):
    """Standalone application to validate/check Illumina sample sheet"""
    name = kwargs["name"]
    if kwargs["check"]:
        iem = SampleSheetFactory(name)
        iem.validate()
        logger.info("SampleSheet looks correct")
    elif kwargs["full_check"]:
        iem = SampleSheetFactory(name)

        checks = iem.checker()
        for check in checks:
            if check["status"] == "Error":
                try:
                    print(f"\u274C {check['status']}, {check['msg']} {check['caller']}")
                except:
                    print(f"\u274C {check['status']}, {check['msg']} ")

        for check in checks:
            if check["status"] == "Warning":
                print(f"\u26A0 {check['status']}, {check['msg']}")

        for check in checks:
            if check["status"] == "Success":
                print(f"\u2714 {check['status']}, {check['msg']}")

    elif kwargs["extract_adapters"]:
        iem = SampleSheetFactory(name)
        iem.to_fasta()
    elif kwargs["quick_fix"]:
        iem = SampleSheetFactory(name)
        if kwargs["output"]:
            filename = kwargs["output"]
        else:  # pragma: no cover
            filename = name + ".fixed"
        logger.info("Saving fixed version in {}".format(filename))
        iem.quick_fix(output_filename=filename)

1	# This file is part of Sequana software
2	#
3	# Copyright (c) 2016-2020 - Sequana Development Team
4	#
5	# Distributed under the terms of the 3-clause BSD license.
6	# The full license is in the LICENSE file, distributed with this software.
7	#
8	# website: https://github.com/sequana/sequana
9	# documentation: http://sequana.readthedocs.io
10	#
11	##############################################################################
12	import colorlog	3✔
13	import rich_click as click	3✔
14
15	from sequana.iem import SampleSheetFactory	3✔
16	from sequana.scripts.utils import CONTEXT_SETTINGS	3✔
17
18	logger = colorlog.getLogger(__name__)	3✔
19
20
21	@click.command(context_settings=CONTEXT_SETTINGS)	3✔
22	@click.argument("name", type=click.STRING)	3✔
23	@click.option("--check", is_flag=True, help="report validity of the input file")	3✔
24	@click.option("--full-check", is_flag=True, help="report complete report of all checks")	3✔
25	@click.option(	3✔
26	"--extract-adapters",
27	is_flag=True,
28	help="extract adapters from the settings section and save them into a fasta file",
29	)
30	@click.option("--quick-fix", is_flag=True)	3✔
31	@click.option("--output", default=None)	3✔
32	def samplesheet(**kwargs):	3✔
33	"""Standalone application to validate/check Illumina sample sheet"""
34	name = kwargs["name"]	3✔
35	if kwargs["check"]:	3✔
36	iem = SampleSheetFactory(name)	3✔
37	iem.validate()	3✔
38	logger.info("SampleSheet looks correct")	3✔
39	elif kwargs["full_check"]:	3✔
NEW 40	iem = SampleSheetFactory(name)	×
41
42	checks = iem.checker()	×
43	for check in checks:	×
44	if check["status"] == "Error":	×
45	try:	×
46	print(f"\u274C {check['status']}, {check['msg']} {check['caller']}")	×
47	except:	×
48	print(f"\u274C {check['status']}, {check['msg']} ")	×
49
50	for check in checks:	×
51	if check["status"] == "Warning":	×
52	print(f"\u26A0 {check['status']}, {check['msg']}")	×
53
54	for check in checks:	×
55	if check["status"] == "Success":	×
56	print(f"\u2714 {check['status']}, {check['msg']}")	×
57
58	elif kwargs["extract_adapters"]:	3✔
59	iem = SampleSheetFactory(name)	3✔
60	iem.to_fasta()	3✔
61	elif kwargs["quick_fix"]:	3✔
62	iem = SampleSheetFactory(name)	3✔
63	if kwargs["output"]:	3✔
64	filename = kwargs["output"]	3✔
65	else: # pragma: no cover
66	filename = name + ".fixed"
67	logger.info("Saving fixed version in {}".format(filename))	3✔
68	iem.quick_fix(output_filename=filename)	3✔

sequana / sequana / 28578229798

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