-
We use the `BitVector` type to represent ambiguous nucleotides in a sequence.
https://github.com/BioJulia/Bio.jl/blob/0697dc92bc8394d447a6ec3e99454f3d59b2d471/src/seq/nucleotide.jl#L185
What I'm worr…
-
As you mention in JuliaLang/julia#12624, several people have implemented interval types in their packages. I know at least of @dcjones's [IntervalTree](https://github.com/BioJulia/IntervalTrees.jl) pa…
ssfrr updated
8 years ago
-
I was taking a look at http://www.ncbi.nlm.nih.gov/nuccore/NC_010004 and I was surprised that parsing the FASTA file the record was of type AminoAcidSequence instead of DNASequence.
Is there a way to…
-
In Bio.jl, we often extend functions exported from the `Base` module. But as @dcjones said (https://github.com/BioJulia/Bio.jl/pull/85#discussion_r39339225), it is annoying to synchronize method defin…
-
Currently, the development of machine learning tools are in several different packages without little coordination. Consequently, some efforts are repetitive, while some important aspects remain lacki…
-
I'd like to propose the creation of a Gitter chat room and the inclusion of a badge to this repository README, this would allow us to communicate more widely, meet each other, share ideas and get feed…
-
So I was playing a bit with the current `master` branch BioSequences, when I noticed that when loading a big file of repeat masked human genomic regions, 1 out of the first 21 was returned as an Amino…
-
I don't know what's wrong.Please help me.
Pkg.test("Bio")
INFO: Computing test dependencies for Bio...
INFO: Installing YAML v0.1.10
INFO: Testing Bio
WARNING: deprecated syntax "{}" at C:\Users\Mi…
ghost updated
8 years ago
-
Is it correct that stop codons (represented as '*') are not considered a valid part of amino acid sequences? See:
```
julia> Bio.Seq.AminoAcidSequence("PLCFRHHQSRYTGKLL*")
ERROR: * is not a valid ami…
-
Below is review of current `write` an `read` variants in `Base`.
I propose:
- deprecate `readbytes` and `readall`, replace with `read` and `readstring` respectively
- add filename-as-1st-arg support…