bio is a semantic Bioinformatics module that emphasizes a definitive design structure.
go get github.com/sembio/go/...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 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 sembio/go, visit: https://godoc.org/github.com/sembio/go/bio
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 sembio/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.