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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85.71

/sequana/scripts/main/ribodesigner.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 pathlib
import shutil
import sys

import colorlog
import rich_click as click

from sequana.ribodesigner import RiboDesigner
from sequana.scripts.common import teardown
from sequana.scripts.utils import CONTEXT_SETTINGS

logger = colorlog.getLogger(__name__)


# =====================================================================================
# Ribodepletion custom probes designer
# =====================================================================================
@click.command(context_settings=CONTEXT_SETTINGS)
@click.argument("fasta", type=click.Path(exists=True))
@click.argument("gff", type=click.Path(exists=True), default=None, required=False)
@click.option("--output-directory", show_default=True, default="out_ribodesigner", type=click.Path(exists=False))
@click.option(
    "--seq-type", default="rRNA", show_default=True, help="The annotation type (column 3 in gff) to target for probes."
)
@click.option(
    "--max-n-probes", default=384, show_default=True, type=click.INT, help="The maximum number of probes to design."
)
@click.option(
    "--threads", default=4, show_default=True, type=click.INT, help="The number of threads to use for cd-hit-est."
)
@click.option(
    "--identity-step",
    default=0.01,
    show_default=True,
    type=click.FLOAT,
    help="The number of threads to use for cd-hit-est.",
)
@click.option("--output-image", default=None)
@click.option(
    "--force",
    default=False,
    is_flag=True,
    type=click.BOOL,
    show_default=True,
    help="If output directory exists, use this option to erase previous results",
)
def ribodesigner(**kwargs):
    """A tool to design custom ribodepletion probes.

    This uses a reference genome (FASTA file) and the corresponding annotation
    (GFF file). CD-HIT-EST should be installed and in your $PATH.
    """

    if not shutil.which("cd-hit-est"):
        logger.error("cd-hit-est not found in PATH.")
        sys.exit(1)

    RiboDesigner(**kwargs).run()
    if kwargs["output_image"]:
        from pylab import savefig

        savefig("/".join([kwargs["output_directory"], kwargs["output_image"]]))

    teardown(kwargs["output_directory"])

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 pathlib	3✔
13	import shutil	3✔
14	import sys	3✔
15
16	import colorlog	3✔
17	import rich_click as click	3✔
18
19	from sequana.ribodesigner import RiboDesigner	3✔
20	from sequana.scripts.common import teardown	3✔
21	from sequana.scripts.utils import CONTEXT_SETTINGS	3✔
22
23	logger = colorlog.getLogger(__name__)	3✔
24
25
26	# =====================================================================================
27	# Ribodepletion custom probes designer
28	# =====================================================================================
29	@click.command(context_settings=CONTEXT_SETTINGS)	3✔
30	@click.argument("fasta", type=click.Path(exists=True))	3✔
31	@click.argument("gff", type=click.Path(exists=True), default=None, required=False)	3✔
32	@click.option("--output-directory", show_default=True, default="out_ribodesigner", type=click.Path(exists=False))	3✔
33	@click.option(	3✔
34	"--seq-type", default="rRNA", show_default=True, help="The annotation type (column 3 in gff) to target for probes."
35	)
36	@click.option(	3✔
37	"--max-n-probes", default=384, show_default=True, type=click.INT, help="The maximum number of probes to design."
38	)
39	@click.option(	3✔
40	"--threads", default=4, show_default=True, type=click.INT, help="The number of threads to use for cd-hit-est."
41	)
42	@click.option(	3✔
43	"--identity-step",
44	default=0.01,
45	show_default=True,
46	type=click.FLOAT,
47	help="The number of threads to use for cd-hit-est.",
48	)
49	@click.option("--output-image", default=None)	3✔
50	@click.option(	3✔
51	"--force",
52	default=False,
53	is_flag=True,
54	type=click.BOOL,
55	show_default=True,
56	help="If output directory exists, use this option to erase previous results",
57	)
58	def ribodesigner(**kwargs):	3✔
59	"""A tool to design custom ribodepletion probes.
60
61	This uses a reference genome (FASTA file) and the corresponding annotation
62	(GFF file). CD-HIT-EST should be installed and in your $PATH.
63	"""
64
65	if not shutil.which("cd-hit-est"):	3✔
66	logger.error("cd-hit-est not found in PATH.")	×
67	sys.exit(1)	×
68
69	RiboDesigner(**kwargs).run()	3✔
70	if kwargs["output_image"]:	3✔
71	from pylab import savefig	×
72
73	savefig("/".join([kwargs["output_directory"], kwargs["output_image"]]))	×
74
75	teardown(kwargs["output_directory"])	3✔

cokelaer / sequana / 7117302237

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