README
¶
Bio -- Bioinformatics Module
Overview
bio is a semantic Bioinformatics module that emphasizes a definitive design structure.
Installation
go get github.com/bio-ext/bio-go/...
Design Structure
This module is structured intentionally to form a fat tree where each step down the tree asks/answers a new question in the following order:
- Why are you looking into this module? (i.e., the kind of work you are doing)
- How are you hoping to get the job done? (i.e., do you need speed, immutability, simplicity, and so on)
- What are you going to use? (i.e., the what that allows the why for your work)
These questions are very general so a contrived example might be "I need to represent N sequences of DNA with IUPAC ambiguity":
- Why...? Ex: I need sequences (look in
bio/sequencepackage) - How...? Ex: I prefer immutable data structures (look in
.../sequence/immutablepackage) - What...? Ex: I need IUPAC DNA (look in
.../immutable/*iupac*files)
Full path: bio/sequence/immutable/dna_iupac.go to use immutable.NewDnaIupac(...) N times.
This structure should promote quick searches for the why, how, and what that must be answered for every project many times over.
This design means that everything under a directory should implement the interfaces above and inline with it in the tree; for example: everything under bio/sequence implements sequence.Interface and everything under bio/alphabet implements alphabet.Interface and so on.
If more than three levels are deemed necessary the first level will represent some generic functionality, such as in the case of bio/io/fasta/base/fasta.go which is housed under the generic io then answers our three questions fasta (why), base (how), fasta.go (what).
Documentation
Documentation can be built through use of godoc -http=localhost:6060 which then generates documentation accessible through a web browser at localhost:6060. For access to prior to downloading bio-go, visit: https://godoc.org/github.com/bio-ext/bio-go/bio
Testing
Tests can be run through use of go test -v ./... at the root of this repository. Use of the verbose -v flag is recommended as bio-go makes extensive use of property tests, which should provide insight into what can be expected of a given implementation.
All tests, benchmarks, and examples are run continuously and can be viewed on Travis CI.
Directories
¶
| Path | Synopsis |
|---|---|
|
Package bio is a library representing Bioinformatics solutions.
|
Package bio is a library representing Bioinformatics solutions. |
|
alphabet
Package alphabet defines the abstract interface for a biological alphabet.
|
Package alphabet defines the abstract interface for a biological alphabet. |
|
alphabet/hashmap
Package hashmap is a collection of defined biological alphabets such as DNA, RNA, and Protein
|
Package hashmap is a collection of defined biological alphabets such as DNA, RNA, and Protein |
|
data
Package data is commonly referenced data such as lookup tables
|
Package data is commonly referenced data such as lookup tables |
|
data/codon
Package codon contains 31 DNA to Protein translation tables.
|
Package codon contains 31 DNA to Protein translation tables. |
|
data/quality
Package quality handles scores used to encode quality of a sequence
|
Package quality handles scores used to encode quality of a sequence |
|
io
Package io is a collection of IO operations with a focus on common standard formats
|
Package io is a collection of IO operations with a focus on common standard formats |
|
io/fasta
Package fasta handles reading, writing, and utilizing FASTA format
|
Package fasta handles reading, writing, and utilizing FASTA format |
|
io/fasta/base
Package base is a basic implementation of FASTA reading
|
Package base is a basic implementation of FASTA reading |
|
io/fastq
Package fastq handles reading, writing, and utilizing FASTQ format
|
Package fastq handles reading, writing, and utilizing FASTQ format |
|
sequence
Package sequence defines the abstract interface for a biological sequence.
|
Package sequence defines the abstract interface for a biological sequence. |
|
sequence/immutable
Package immutable is an implementation of biological sequences that have immutability.
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Package immutable is an implementation of biological sequences that have immutability. |
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sequence/mutable
Package mutable is an implementation of biological sequences that mutate internally.
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Package mutable is an implementation of biological sequences that mutate internally. |
|
test
Package test defines any testing constants or functions used to validate assumptions.
|
Package test defines any testing constants or functions used to validate assumptions. |
|
utils
Package utils is a collection of helpful utilities
|
Package utils is a collection of helpful utilities |