biostuff

module

v0.1.18 Latest Latest Go to latest Published: Jul 8, 2022 License: MIT

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Valid go.mod file

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Computational biology packages for Go, with emphasis on minimialism.

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

Data formats
- bed
- fasta
- fastq
- newick
- 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

Found a bug? Got feedback? Questions? Feel free to open an issue and let me know!

Path	Synopsis
align Package align provides functionality for aligning sequences.	Package align provides functionality for aligning sequences.
genncbi Command genncbi generates substitution matrices from NCBI text files.	Command genncbi generates substitution matrices from NCBI text files.
formats
bed Package bed decodes and encodes BED files.	Package bed decodes and encodes BED files.
fasta Package fasta decodes and encodes fasta files.	Package fasta decodes and encodes 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 decodes and encodes fastq files.	Package fastq decodes and encodes fastq files.
newick Package newick decodes and encodes Newick-formatted trees.	Package newick decodes and encodes Newick-formatted trees.
sam Package sam decodes and encodes SAM files.	Package sam decodes and encodes SAM files.
smtext Package smtext handles text representations of substitution matrices.	Package smtext handles text representations of substitution matrices.
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.