biostuff

module

v0.1.11 Latest Latest Go to latest Published: Oct 6, 2021 License: MIT

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

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

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

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

Path	Synopsis
align Package align provides functionality for aligning sequences.	Package align provides functionality for aligning sequences.
smtext Package smtext handles text representations of substitution matrices.	Package smtext handles text representations of substitution matrices.
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.
sam Package sam parses SAM files.	Package sam parses SAM files.
regions Package regions provides an index for searching on intervals.	Package regions provides an index for searching on intervals.
sequtil Package sequtil provides functions for processing genetic sequences.	Package sequtil provides functions for processing genetic sequences.
trie Package trie provides a prefix tree implementation.	Package trie provides a prefix tree implementation.