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Project: mgnify-pipelines-toolkit
Version: 1.0.4
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METADATA · WHEEL · RECORD · top_level.txt · entry_points.txt

METADATA

Metadata-Version: 2.4
Name: mgnify_pipelines_toolkit
Version: 1.0.4
Summary: Collection of scripts and tools for MGnify pipelines
Author-Email: MGnify team <metagenomics-help[at]ebi.ac.uk>
License: Apache Software License 2.0
Keywords: bioinformatics,pipelines,metagenomics
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Requires-Dist: biopython (>=1.85)
Requires-Dist: numpy (<3,>=2.2.4)
Requires-Dist: pandas (<3,>=2.2.3)
Requires-Dist: regex (>=2024.11.6)
Requires-Dist: requests (<3,>=2.32.3)
Requires-Dist: click (<9,>=8.1.8)
Requires-Dist: pandera (<0.24,>=0.23.1)
Requires-Dist: pyfastx (<3,>=2.2.0)
Requires-Dist: intervaltree (<4,>=3.1.0)
Requires-Dist: pytest (<9,>=8.3.5); extra == "tests"
Requires-Dist: pytest-md (>=0.2.0); extra == "tests"
Requires-Dist: pytest-workflow (==2.1.0); extra == "tests"
Requires-Dist: pre-commit (>=4.2.0); extra == "dev"
Requires-Dist: black (>=25.1.0); extra == "dev"
Requires-Dist: flake8 (>=7.1.2); extra == "dev"
Requires-Dist: pep8-naming (>=0.14.1); extra == "dev"
Provides-Extra: tests
Provides-Extra: dev
Description-Content-Type: text/markdown
Dynamic: license-file
License-File: LICENSE
[Description omitted; length: 4585 characters]

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top_level.txt

mgnify_pipelines_toolkit

entry_points.txt

[console_scripts]
add_rhea_chebi_annotation = mgnify_pipelines_toolkit.analysis.assembly.add_rhea_chebi_annotation:main
antismash_gff_builder = mgnify_pipelines_toolkit.analysis.assembly.antismash_gff_builder:main
are_there_primers = mgnify_pipelines_toolkit.analysis.amplicon.are_there_primers:main
assess_inflection_point_mcp = mgnify_pipelines_toolkit.analysis.amplicon.assess_inflection_point_mcp:main
assess_mcp_proportions = mgnify_pipelines_toolkit.analysis.amplicon.assess_mcp_proportions:main
classify_var_regions = mgnify_pipelines_toolkit.analysis.amplicon.classify_var_regions:main
combined_gene_caller_merge = mgnify_pipelines_toolkit.analysis.assembly.combined_gene_caller_merge:main
convert_cmscan_to_cmsearch_tblout = mgnify_pipelines_toolkit.analysis.shared.convert_cmscan_to_cmsearch_tblout:main
dwc_summary_generator = mgnify_pipelines_toolkit.analysis.shared.dwc_summary_generator:main
fasta_to_delimited = mgnify_pipelines_toolkit.utils.fasta_to_delimited:main
fastq_suffix_header_check = mgnify_pipelines_toolkit.analysis.shared.fastq_suffix_header_check:main
find_mcp_inflection_points = mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main
generate_gaf = mgnify_pipelines_toolkit.analysis.assembly.generate_gaf:main
genomes_extract_bacterial_rrnas_as_tsv = mgnify_pipelines_toolkit.analysis.genomes.rna.extract_bacterial_rrnas_as_tsv:main
genomes_extract_rrnas_as_fasta = mgnify_pipelines_toolkit.analysis.genomes.rna.extract_rrnas_as_fasta:main
genomes_extract_trnas = mgnify_pipelines_toolkit.analysis.genomes.rna.extract_trnas:main
get_mpt_version = mgnify_pipelines_toolkit.utils.get_mpt_version:main
get_subunits = mgnify_pipelines_toolkit.analysis.shared.get_subunits:main
get_subunits_coords = mgnify_pipelines_toolkit.analysis.shared.get_subunits_coords:main
krona_txt_from_cat_classification = mgnify_pipelines_toolkit.analysis.assembly.krona_txt_from_cat_classification:main
library_strategy_check = mgnify_pipelines_toolkit.analysis.shared.library_strategy_check:main
make_asv_count_table = mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main
mapseq2biom = mgnify_pipelines_toolkit.analysis.shared.mapseq2biom:main
mapseq_to_asv_table = mgnify_pipelines_toolkit.analysis.amplicon.mapseq_to_asv_table:main
markergene_study_summary = mgnify_pipelines_toolkit.analysis.shared.markergene_study_summary:main
primer_val_classification = mgnify_pipelines_toolkit.analysis.amplicon.primer_val_classification:main
remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main
rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main
standard_primer_matching = mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_matching:main
study_summary_generator = mgnify_pipelines_toolkit.analysis.shared.study_summary_generator:cli
summarise_goslims = mgnify_pipelines_toolkit.analysis.assembly.summarise_goslims:main