7117302237

Committed 06 Dec 2023 04:23PM UTC coverage: 75.482% (+1.8%) from 73.729%

Build # 7117302237

Build Type

push

github

Committed by

cokelaer

Commit Message

Update version

Run Details

13709 of 18162 relevant lines covered (75.48%)

2.26 hits per line

Source File
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75.0

/sequana/scripts/main/feature_count.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.scripts.utils import CONTEXT_SETTINGS, common_logger

logger = colorlog.getLogger(__name__)


@click.command(context_settings=CONTEXT_SETTINGS)
@click.option(
    "--pattern",
    help="The pattern of the feature counts files to merge",
    show_default=True,
    default="*feature.out",
)
@click.option(
    "--output",
    help="The output filename where to save the merged counts",
    show_default=True,
    default="all_features.out",
)
@common_logger
def feature_counts(**kwargs):
    """Merge several feature counts files into one file"""
    from sequana.featurecounts import FeatureCountMerger

    fcm = FeatureCountMerger(kwargs["pattern"])
    fcm.to_tsv(output_filename=kwargs["output"])

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.scripts.utils import CONTEXT_SETTINGS, common_logger	3✔
16
17	logger = colorlog.getLogger(__name__)	3✔
18
19
20	@click.command(context_settings=CONTEXT_SETTINGS)	3✔
21	@click.option(	3✔
22	"--pattern",
23	help="The pattern of the feature counts files to merge",
24	show_default=True,
25	default="*feature.out",
26	)
27	@click.option(	3✔
28	"--output",
29	help="The output filename where to save the merged counts",
30	show_default=True,
31	default="all_features.out",
32	)
33	@common_logger	3✔
34	def feature_counts(**kwargs):	3✔
35	"""Merge several feature counts files into one file"""
36	from sequana.featurecounts import FeatureCountMerger	×
37
38	fcm = FeatureCountMerger(kwargs["pattern"])	×
39	fcm.to_tsv(output_filename=kwargs["output"])	×

cokelaer / sequana / 7117302237

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