Comments (3)
tomoakin
commented on June 13, 2024
The following patch speeds up for about 80 fold:
This is new and accuracy needs be checked.
http://github.com/tomoakin/bioruby/commit/f236c855b0a9f4fca49494a70e66a5cc33585b70
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tomoakin
commented on June 13, 2024
Previous one failed in some unit tests. The latest code is and will be on the branch
http://github.com/tomoakin/bioruby/tree/1.4.1RE
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ngoto
commented on June 13, 2024
I modified the tomoakin's patch and optimized more.
ngoto@f062b5f
With the new code ,in my machine, cutting of 5Mbp sequence takes only 24 seconds.
The code will be included in the next release, although with some incompatible internal data structure changes.
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Related Issues (20)
- Bioruby site is down! HOT 7
- bio-1.5.0/lib/bio/db.rb:267:in `gsub': invalid byte sequence in UTF-8 (ArgumentError) HOT 1
- Change base URLs for NCBI services to use https instead of http HOT 8
- HTTPS Proxy HOT 1
- Rails 5 eager loading (gem broken in Rails 5+) HOT 2
- OBF mail list issues HOT 6
- Some classes are not explained in the yard document HOT 2
- Bio::Blast exec_genomenet: cannot understand response (RuntimeError) HOT 6
- Is there a way to get KEGG pathway images? HOT 1
- Is there a way to get KEGG pathway images? HOT 2
- Issue about no file found HOT 10
- Bio::Blast known bug... any timeline? HOT 1
- change IDs in a GFF3
- cutting by restriction enzymes with asymmetric target HOT 2
- required libraries not loaded HOT 1
- Request for technical discussions feature on this repository HOT 5
- On Ruby 3.0, methods in a subclass of String return String instead of the subclass instance HOT 9
- Fix Gem::Specification dep warnings HOT 1
- bioruby shell seems broken HOT 2
- Bug in UniProtKB class with ft field HOT 4
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