7762707327

Committed 02 Feb 2024 11:27PM UTC coverage: 75.585% (-0.01%) from 75.599%

Build # 7762707327

Build Type

push

github

Committed by

cokelaer

Commit Message

Fix test

Run Details

13829 of 18296 relevant lines covered (75.58%)

3.02 hits per line

Source File
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65.12

/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 IEM
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="")
@click.option("--full-check", is_flag=True)
@click.option("--extract-adapters", is_flag=True)
@click.option("--quick-fix", is_flag=True)
@click.option("--output", default=None)
def samplesheet(**kwargs):
    """Utilities to manipulate sample sheet"""
    name = kwargs["name"]
    if kwargs["check"]:
        iem = IEM(name)
        iem.validate()
        logger.info("SampleSheet looks correct")
    elif kwargs["full_check"]:
        iem = IEM(name)

        try:
            iem.validate()
        except SystemExit:
            pass

        checks = iem.checker()
        for check in checks:
            if check["status"] == "Error":
                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 = IEM(name)
        iem.to_fasta()
    elif kwargs["quick_fix"]:
        iem = IEM(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	4✔
13	import rich_click as click	4✔
14
15	from sequana.iem import IEM	4✔
16	from sequana.scripts.utils import CONTEXT_SETTINGS	4✔
17
18	logger = colorlog.getLogger(__name__)	4✔
19
20
21	@click.command(context_settings=CONTEXT_SETTINGS)	4✔
22	@click.argument("name", type=click.STRING)	4✔
23	@click.option("--check", is_flag=True, help="")	4✔
24	@click.option("--full-check", is_flag=True)	4✔
25	@click.option("--extract-adapters", is_flag=True)	4✔
26	@click.option("--quick-fix", is_flag=True)	4✔
27	@click.option("--output", default=None)	4✔
28	def samplesheet(**kwargs):	4✔
29	"""Utilities to manipulate sample sheet"""
30	name = kwargs["name"]	4✔
31	if kwargs["check"]:	4✔
32	iem = IEM(name)	4✔
33	iem.validate()	4✔
34	logger.info("SampleSheet looks correct")	4✔
35	elif kwargs["full_check"]:	4✔
36	iem = IEM(name)	×
37
38	try:	×
39	iem.validate()	×
40	except SystemExit:	×
41	pass	×
42
43	checks = iem.checker()	×
44	for check in checks:	×
45	if check["status"] == "Error":	×
46	print(f"\u274C {check['status']}, {check['msg']}")	×
47
48	for check in checks:	×
49	if check["status"] == "Warning":	×
50	print(f"\u26A0 {check['status']}, {check['msg']}")	×
51
52	for check in checks:	×
53	if check["status"] == "Success":	×
54	print(f"\u2714 {check['status']}, {check['msg']}")	×
55
56	elif kwargs["extract_adapters"]:	4✔
57	iem = IEM(name)	4✔
58	iem.to_fasta()	4✔
59	elif kwargs["quick_fix"]:	4✔
60	iem = IEM(name)	4✔
61	if kwargs["output"]:	4✔
62	filename = kwargs["output"]	4✔
63	else: # pragma: no cover
64	filename = name + ".fixed"
65	logger.info("Saving fixed version in {}".format(filename))	4✔
66	iem.quick_fix(output_filename=filename)	4✔

cokelaer / sequana / 7762707327

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