genomicspy 0.2.1

Tools for manipulating vcfs doing genomics work

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.