Comments (1)
seq_io
automatically grows the internal buffer when sequences are longer, this should work out of the box. Buffer growth can also be configured, e.g. an upper limit can be set (may make sense, in 0.4-alpha I introduced such a limit by default). Due to the design of this library, the sequence record always needs to fit into the buffer completely.
Assuming that your input is FASTA, you could iterate over sequence lines using seq_lines(), which would be the fastest, but probably complicated with sliding window analysis when reaching line ends. The full (contiguous) sequence is e.g. accessed using full_seq(). In the latest alpha release, there is also full_seq_given(), which allows avoiding unnecessary and slow allocations. If you need to access several sequences from the alignment at once, you need to copy them somewhere anyway. The fastest in 0.4 would be clone_into_owned().
I hope that this answers your question...
from seq_io.
Related Issues (11)
- parallel reading 10G fasta/fastq file HOT 5
- Open to a PR for impl Display (or Debug) etc.? HOT 1
- An error in record.rs in core HOT 2
- Issue when get the size of sequence length in reference genome file HOT 1
- Future incompatibility with buf_redux HOT 2
- curious error when reading fastq.gz files (maybe not an issue) HOT 2
- Depends on old crossbeam HOT 1
- Reading gz files? HOT 3
- write_* takes ownership of Writer HOT 3
- Release of 0.4.0 HOT 4
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 seq_io.