11808924106

Committed 17 Oct 2024 01:01PM UTC coverage: 73.623% (-1.2%) from 74.78%

Build # 11808924106

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #861 from cokelaer/dev

add somy, improved coverage

Run Details

204 of 550 new or added lines in 19 files covered. (37.09%)

22 existing lines in 4 files now uncovered.

14009 of 19028 relevant lines covered (73.62%)

2.94 hits per line

Source File
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86.67

/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(
    "--method", type=click.Choice(["original", "greedy", "spiral", "simple"]), default="original", 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(
    "--force-clustering",
    default=False,
    is_flag=True,
    type=click.BOOL,
    show_default=True,
    required=False,
    help="By default, if number of probes is above 384 (see --max-n-probes) a clustering is performed using an identity threshold (with --identity-step). If not, no clustering is done. You may force the clustering using this option.",
)
@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 identity parameters used by 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. Try to install it with conda, or damona (damona.readthedocs.io)")
        sys.exit(1)

    RiboDesigner(**kwargs).run(method=kwargs["method"])

    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	4✔
13	import shutil	4✔
14	import sys	4✔
15
16	import colorlog	4✔
17	import rich_click as click	4✔
18
19	from sequana.ribodesigner import RiboDesigner	4✔
20	from sequana.scripts.common import teardown	4✔
21	from sequana.scripts.utils import CONTEXT_SETTINGS	4✔
22
23	logger = colorlog.getLogger(__name__)	4✔
24
25
26	# =====================================================================================
27	# Ribodepletion custom probes designer
28	# =====================================================================================
29	@click.command(context_settings=CONTEXT_SETTINGS)	4✔
30	@click.argument("fasta", type=click.Path(exists=True))	4✔
31	@click.argument("gff", type=click.Path(exists=True), default=None, required=False)	4✔
32	@click.option(	4✔
33	"--method", type=click.Choice(["original", "greedy", "spiral", "simple"]), default="original", required=False
34	)
35	@click.option("--output-directory", show_default=True, default="out_ribodesigner", type=click.Path(exists=False))	4✔
36	@click.option(	4✔
37	"--seq-type", default="rRNA", show_default=True, help="The annotation type (column 3 in gff) to target for probes."
38	)
39	@click.option(	4✔
40	"--max-n-probes", default=384, show_default=True, type=click.INT, help="The maximum number of probes to design."
41	)
42	@click.option(	4✔
43	"--force-clustering",
44	default=False,
45	is_flag=True,
46	type=click.BOOL,
47	show_default=True,
48	required=False,
49	help="By default, if number of probes is above 384 (see --max-n-probes) a clustering is performed using an identity threshold (with --identity-step). If not, no clustering is done. You may force the clustering using this option.",
50	)
51	@click.option(	4✔
52	"--threads", default=4, show_default=True, type=click.INT, help="The number of threads to use for cd-hit-est."
53	)
54	@click.option(	4✔
55	"--identity-step",
56	default=0.01,
57	show_default=True,
58	type=click.FLOAT,
59	help="The identity parameters used by cd-hit-est.",
60	)
61	@click.option("--output-image", default=None)	4✔
62	@click.option(	4✔
63	"--force",
64	default=False,
65	is_flag=True,
66	type=click.BOOL,
67	show_default=True,
68	help="If output directory exists, use this option to erase previous results",
69	)
70	def ribodesigner(**kwargs):	4✔
71	"""A tool to design custom ribodepletion probes.
72
73	This uses a reference genome (FASTA file) and the corresponding annotation
74	(GFF file). CD-HIT-EST should be installed and in your $PATH.
75	"""
76	if not shutil.which("cd-hit-est"):	4✔
NEW 77	logger.error("cd-hit-est not found in PATH. Try to install it with conda, or damona (damona.readthedocs.io)")	×
78	sys.exit(1)	×
79
80	RiboDesigner(**kwargs).run(method=kwargs["method"])	4✔
81
82	if kwargs["output_image"]:	4✔
83	from pylab import savefig	×
84
85	savefig("/".join([kwargs["output_directory"], kwargs["output_image"]]))	×
86
87	teardown(kwargs["output_directory"])	4✔

sequana / sequana / 11808924106

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