genmod 3.8.2__tar.gz → 3.8.3__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {genmod-3.8.2/genmod.egg-info → genmod-3.8.3}/PKG-INFO +2 -1
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/compound_scorer.py +2 -0
- {genmod-3.8.2 → genmod-3.8.3/genmod.egg-info}/PKG-INFO +2 -1
- {genmod-3.8.2 → genmod-3.8.3}/genmod.egg-info/requires.txt +1 -0
- {genmod-3.8.2 → genmod-3.8.3}/setup.py +3 -2
- {genmod-3.8.2 → genmod-3.8.3}/LICENSE.txt +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/MANIFEST.in +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/README.md +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/dominant_trio.ped +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/multi_allele_example.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/multi_family.ped +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/recessive_trio.ped +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_1000G.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_1000G.vcf.gz +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_1000G.vcf.gz.tbi +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_1000G_CADD.tsv.gz +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_1000G_CADD.tsv.gz.tbi +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_CADD.tsv.gz +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_CADD.tsv.gz.tbi +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_dbNSFP.txt.gz +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_dbNSFP.txt.gz.tbi +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/small_vep.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/test_phased_compounds.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/test_vcf.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/test_vcf_regions.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/test_vcf_regions_models.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/examples/test_vcf_regions_models_scored.vcf +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/fix_variant.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/genetic_models.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/make_haploblocks.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/model_score.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/models/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/models/compound_model.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/models/dominant_model.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/models/recessive_model.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/models/x_models.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_models/variant_annotator.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_regions/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_regions/get_features.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_regions/parse_annotations.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_variants/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_variants/add_annotations.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_variants/annotate.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotate_variants/read_tabix_files.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotations/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotations/ensembl_genes_37.txt.gz +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/annotations/ensembl_genes_38.txt.gz +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/analyze.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/annotate_models.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/annotate_variant.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/base.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/filter_variants.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/genmod_sort.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/score_compounds.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/score_variants.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/summarize_variants.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/commands/utils.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/configs/genmod_test.v1.5.ini +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/configs/rank_model_cmms_v1.7.ini +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/configs/rank_model_cmms_v1.9.ini +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/errors/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/errors/warning.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/log.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/cap_rank_score_to_min_bound.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/check_plugins.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/config_parser.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/rank_score_variant_definitions.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/score_function.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/score_variants/score_variant.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/check_individuals.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/get_batches.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/get_features.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/get_priority.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/is_number.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/pair_generator.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/utils/variant_printer.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/__init__.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/add_metadata.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/add_variant_information.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/check_info_header.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/genotype.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/get_genotypes.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/header_parser.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/parse_variant.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/print_headers.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/print_variants.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod/vcf_tools/sort_variants.py +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod.egg-info/SOURCES.txt +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod.egg-info/dependency_links.txt +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod.egg-info/entry_points.txt +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/genmod.egg-info/top_level.txt +0 -0
- {genmod-3.8.2 → genmod-3.8.3}/setup.cfg +0 -0
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Metadata-Version: 2.1
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Name: genmod
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Version: 3.8.
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Version: 3.8.3
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Summary: Annotate genetic inheritance models in variant files
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Home-page: http://github.com/moonso/genmod
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Author: Mans Magnusson
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Requires-Dist: intervaltree>=3.1.0
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Requires-Dist: extract_vcf>=0.5
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Requires-Dist: vcftoolbox>=1.5.1
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Requires-Dist: six>=1.16.0
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Tool for annotating patterns of genetic inheritance in Variant Call Format (VCF) files.
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new_compound = "{0}>{1}".format(compound_id, compound_score)
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scored_compound_list.append(new_compound)
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# Sort compound variants lexicographically
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scored_compound_list.sort()
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new_compound_string = "{0}:{1}".format(
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compound_family_id, '|'.join(scored_compound_list))
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Metadata-Version: 2.1
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Name: genmod
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Version: 3.8.
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Version: 3.8.3
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Summary: Annotate genetic inheritance models in variant files
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Home-page: http://github.com/moonso/genmod
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Author: Mans Magnusson
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Requires-Dist: six>=1.16.0
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Tool for annotating patterns of genetic inheritance in Variant Call Format (VCF) files.
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long_description = 'Tool for annotating patterns of genetic inheritance in Variant Call Format (VCF) files.'
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setup(name='genmod',
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version='3.8.
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version='3.8.3',
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description='Annotate genetic inheritance models in variant files',
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author = 'Mans Magnusson',
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author_email = 'mans.magnusson@scilifelab.se',
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'configobj >= 5.0.8',
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'intervaltree >= 3.1.0',
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'extract_vcf >= 0.5',
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'six >= 1.16.0',
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],
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packages=find_packages(
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exclude=('tests*', 'docs', 'examples', 'configs')
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