biostuff

module
Version: v0.1.17 Latest Latest
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Published: Nov 18, 2021 License: MIT

README

biostuff

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go get github.com/fluhus/biostuff/...

Pure Go packages for handling biological data. Minimal and efficient.

Package Overview

  • Data formats
  • Nucleotide & amino-acid sequence utilities
  • Algorithms & data structures
    • align sequence alignment logic
    • regions an index for interval (genes, etc.) overlap lookup
    • trie a prefix tree for sequence lookups

Help or Get Help

I'd love to hear from you. Open an issue if you find a bug or have any feedback or question.

Directories

Path Synopsis
Package align provides functionality for aligning sequences.
Package align provides functionality for aligning sequences.
formats
bed
Package bed parses BED files.
Package bed parses BED files.
fasta
Package fasta parses fasta files.
Package fasta parses fasta files.
fasta/fastaserver
Command fastaserver is a server that serves sequences from a fasta file.
Command fastaserver is a server that serves sequences from a fasta file.
fastq
Package fastq parses fastq files.
Package fastq parses fastq files.
newick
Package newick handles reading and writing Newick-formatted trees.
Package newick handles reading and writing Newick-formatted trees.
sam
Package sam parses SAM files.
Package sam parses SAM files.
smtext
Package smtext handles text representations of substitution matrices.
Package smtext handles text representations of substitution matrices.
Package regions provides an index for searching on intervals.
Package regions provides an index for searching on intervals.
Package sequtil provides functions for processing genetic sequences.
Package sequtil provides functions for processing genetic sequences.
Package trie provides a prefix tree implementation.
Package trie provides a prefix tree implementation.

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