Bed Python Packages

deeptoolsintervals

A python library for constructing interval trees with associated exon/annotation information

bedspec

An HTS-specs compliant BED toolkit

fuc

Frequently used commands in bioinformatics

pygtftk

A python package and a set of shell commands to handle GTF files

vcf2variants

Extract coverage information from gVCF and variants from VCF files and output in tabular format.

py-packbed

pack a .bed into overlapping components

bioartifact

Lightweight, agent-friendly inspection and contract validation for bioinformatics artifacts.

genome-format-converters

A unified Python CLI for 30 bioinformatics file-format conversions (VCF, GFF3, GTF, BED, GenBank, FASTA, FASTQ, BAM, EIGENSTRAT, PLINK, MAF, MUMmer, HMMER, Newick) with consistent flags, batch mode, and a published Stage 1 benchmark vs convertf, plink2, AGAT, gffread, UCSC, EMBOSS, pyhmmer.

prooverlap

ProOvErlap - Assessing feature proximity/overlap and testing statistical significance from genomic intervals

plink-bed-reader

Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in Python.

soda-gallery

Python-based UCSC genome browser snapshot-taker and gallery-maker

pygvcf2coverage

Extract coverage information from gVCF and variants from VCF files and output in tabular format.