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

98.18

/sequana/scripts/main/main.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 rich_click as click

from sequana import version
from sequana.scripts.utils import CONTEXT_SETTINGS

from .biomart import biomart
from .enrichment_kegg import enrichment_kegg
from .enrichment_panther import enrichment_panther
from .enrichment_uniprot import enrichment_uniprot
from .fasta import fasta
from .fastq import fastq
from .feature_count import feature_counts
from .g4hunter import g4hunter
from .gff_to_gtf import gff_to_gtf
from .gff_to_light_gff import gff_to_light_gff
from .gtf_fixer import gtf_fixer
from .lane_merging import lane_merging
from .mapping import mapping
from .ribodesigner import ribodesigner
from .rnadiff import rnadiff
from .rnaseq_compare import rnaseq_compare
from .salmon import salmon_cli
from .samplesheet import samplesheet
from .summary import summary
from .taxonomy import taxonomy
from .variants_comparison import variants_comparison

click.rich_click.USE_MARKDOWN = True
click.rich_click.SHOW_METAVARS_COLUMN = False
click.rich_click.APPEND_METAVARS_HELP = True
click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"
click.rich_click.SHOW_ARGUMENTS = True
click.rich_click.FOOTER_TEXT = "Authors: Thomas Cokelaer, Dimitri Desvillechabrol, Etienne Kornobis -- Documentation: http://sequana.readthedocs.io -- Issues: http://github.com/sequana/sequana"


@click.group(context_settings=CONTEXT_SETTINGS)
@click.version_option(version=version)
def main(**kwargs):
    """This is the main entry point for a set of Sequana applications.

    Pipelines such as sequana_rnaseq, sequana_variant_calling have their own
    application and help.

    In addition, more advanced tools such as sequana_taxonomy or
    sequana_coverage have their own standalone.


    To setup completion, type this command depending on your shell (bash):

        eval "$(_SEQUANA_COMPLETE=bash_source sequana)"
        eval "$(_SEQUANA_COMPLETE=source_zsh sequana)"
        eval (env _SEQUANA_COMPLETE=source_fish sequana)

    """
    pass


main.add_command(biomart)
main.add_command(enrichment_kegg)
main.add_command(enrichment_panther)
main.add_command(enrichment_uniprot)
main.add_command(fastq)
main.add_command(fasta)
main.add_command(feature_counts)
main.add_command(g4hunter)
main.add_command(gff_to_gtf)
main.add_command(gff_to_light_gff)
main.add_command(gtf_fixer)
main.add_command(lane_merging)
main.add_command(mapping)
main.add_command(ribodesigner)
main.add_command(rnadiff)
main.add_command(rnaseq_compare)
main.add_command(salmon_cli, name="salmon")
main.add_command(samplesheet)
main.add_command(summary)
main.add_command(taxonomy)
main.add_command(variants_comparison)

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 rich_click as click	3✔
13
14	from sequana import version	3✔
15	from sequana.scripts.utils import CONTEXT_SETTINGS	3✔
16
17	from .biomart import biomart	3✔
18	from .enrichment_kegg import enrichment_kegg	3✔
19	from .enrichment_panther import enrichment_panther	3✔
20	from .enrichment_uniprot import enrichment_uniprot	3✔
21	from .fasta import fasta	3✔
22	from .fastq import fastq	3✔
23	from .feature_count import feature_counts	3✔
24	from .g4hunter import g4hunter	3✔
25	from .gff_to_gtf import gff_to_gtf	3✔
26	from .gff_to_light_gff import gff_to_light_gff	3✔
27	from .gtf_fixer import gtf_fixer	3✔
28	from .lane_merging import lane_merging	3✔
29	from .mapping import mapping	3✔
30	from .ribodesigner import ribodesigner	3✔
31	from .rnadiff import rnadiff	3✔
32	from .rnaseq_compare import rnaseq_compare	3✔
33	from .salmon import salmon_cli	3✔
34	from .samplesheet import samplesheet	3✔
35	from .summary import summary	3✔
36	from .taxonomy import taxonomy	3✔
37	from .variants_comparison import variants_comparison	3✔
38
39	click.rich_click.USE_MARKDOWN = True	3✔
40	click.rich_click.SHOW_METAVARS_COLUMN = False	3✔
41	click.rich_click.APPEND_METAVARS_HELP = True	3✔
42	click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"	3✔
43	click.rich_click.SHOW_ARGUMENTS = True	3✔
44	click.rich_click.FOOTER_TEXT = "Authors: Thomas Cokelaer, Dimitri Desvillechabrol, Etienne Kornobis -- Documentation: http://sequana.readthedocs.io -- Issues: http://github.com/sequana/sequana"	3✔
45
46
47	@click.group(context_settings=CONTEXT_SETTINGS)	3✔
48	@click.version_option(version=version)	3✔
49	def main(**kwargs):	3✔
50	"""This is the main entry point for a set of Sequana applications.
51
52	Pipelines such as sequana_rnaseq, sequana_variant_calling have their own
53	application and help.
54
55	In addition, more advanced tools such as sequana_taxonomy or
56	sequana_coverage have their own standalone.
57
58
59	To setup completion, type this command depending on your shell (bash):
60
61	eval "$(_SEQUANA_COMPLETE=bash_source sequana)"
62	eval "$(_SEQUANA_COMPLETE=source_zsh sequana)"
63	eval (env _SEQUANA_COMPLETE=source_fish sequana)
64
65	"""
66	pass	×
67
68
69	main.add_command(biomart)	3✔
70	main.add_command(enrichment_kegg)	3✔
71	main.add_command(enrichment_panther)	3✔
72	main.add_command(enrichment_uniprot)	3✔
73	main.add_command(fastq)	3✔
74	main.add_command(fasta)	3✔
75	main.add_command(feature_counts)	3✔
76	main.add_command(g4hunter)	3✔
77	main.add_command(gff_to_gtf)	3✔
78	main.add_command(gff_to_light_gff)	3✔
79	main.add_command(gtf_fixer)	3✔
80	main.add_command(lane_merging)	3✔
81	main.add_command(mapping)	3✔
82	main.add_command(ribodesigner)	3✔
83	main.add_command(rnadiff)	3✔
84	main.add_command(rnaseq_compare)	3✔
85	main.add_command(salmon_cli, name="salmon")	3✔
86	main.add_command(samplesheet)	3✔
87	main.add_command(summary)	3✔
88	main.add_command(taxonomy)	3✔
89	main.add_command(variants_comparison)	3✔

cokelaer / sequana / 7117302237

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

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