Tools for manipulating vcfs doing genomics work
Project description
Tools for manipulating vcfs doing genomics work
Features
Classes:
Chunk: for handling chunks of vcfpy.Record objects
Saver: to save Chunks and vcfpy.Record objects
Types:
SeqType
Methods and constants:
allele_msa: multiple sequence alignments operations
find_read_msas
gen_variants_df
parse_alignments
alleles: manipulating and filling in alleles and variants
combine_ivrs_variants
calc_circular
calc_end_pos
gen_ivrs
check_overlap
gen_alleles_for_chrom_vcf
gen_alleles_from_variants_df
alleles2fastas: converting allele data to fasta sequences
check_fasta_seq_coverage
get_seqlen
infer_entry_name
read_alleles_gts_from_variants
read_alleles_gts_from_vcf
write_fasta_seq
regions: reading and parsing GFF3 and region-feature info
consolidate_gff3
parse_gff3
select_regions
GFF3_COLS
trim: trim alleles or sequences
trim_alleles
trim_allele_seqs
vcf: read VCFs
get_entry_data
parse_records_generator
VCF_COLS
VCF_DEFAULT_DICT
Free software: MIT license
Documentation: https://genomicspy.readthedocs.io.
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
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