Comments (2)
The documentation mentions these
LongDNASeq([x for (x, _) in aln]) # create aligned `s1` with gaps
LongDNASeq([y for (_, y) in aln]) # create aligned `s2` with gaps
which can simply be written into small functions:
seq(aln::PairwiseAlignment) = LongDNASeq([y for (y, _) in aln])
ref(aln::PairwiseAlignment) = LongDNASeq([x for (_, x) in aln])
depending on which you determine to be reference and query you'd have to change the functionnames.
from bioalignments.jl.
The above mentioned gives you the gapped strings, to obtain the original sequences again you can do
aln.a.seq
and aln.b
.
I agree that some convenience functions would be nice though.
from bioalignments.jl.
Related Issues (20)
- Inconsistent when aligning distinct sequence types HOT 1
- `ref2seq` returns a position outside of the sequence length
- What does the two integer fields in `Alignment` do? HOT 1
- The API of accessing fields of BioAlignments
- Bug in `OverlapAlignment` HOT 1
- OP_BACK has no use? HOT 2
- Lack of an article to cite BioAlignments.jl HOT 1
- TagBot not triggering.
- TagBot trigger issue HOT 5
- `AlignmentAnchor` method signature HOT 1
- Extract start and end positions from a PairwiseAlignment HOT 1
- Do these methods work and are they tested? HOT 1
- Alignment of 2 LongAminoAcidSeq with AffineGapScoreModel from docs goes out of bounds HOT 1
- Weird error with `AffineGapScoreModel()`
- Refactor tests
- Outdated documentation for SAM/BAM in BioAlignments is first hit in search HOT 6
- Friendly request to `@deprecate` API changes via semver HOT 2
- Add a `cigar` method and `BioAlignments.Alignment` constructor for XAM.jl optimisation
- [Feature]: Add method to remove sequence match info from cigar HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bioalignments.jl.