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cobot-tools: Biological data file formats and IO
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cobot-tools: Biological data file formats and IO
Please see the README on GitHub at https://github.com/less-wrong/cobot-tools#readme
[Skip to Readme]
Modules
- Bio
- Tools
- Sequence
- CodonOptimization
- Bio.Tools.Sequence.CodonOptimization.Algo
- Bio.Tools.Sequence.CodonOptimization.Constants
- Bio.Tools.Sequence.CodonOptimization.Types
- Primers
- Bio.Tools.Sequence.Primers.Constants
- Bio.Tools.Sequence.Primers.Optimization
- Bio.Tools.Sequence.Primers.Properties
- Bio.Tools.Sequence.Primers.Types
- ViennaRNA
- Bio.Tools.Sequence.ViennaRNA.Cofold
- Bio.Tools.Sequence.ViennaRNA.Fold
- Internal
- Bio.Tools.Sequence.ViennaRNA.Internal.Cofold
- Bio.Tools.Sequence.ViennaRNA.Internal.Fold
- Bio.Tools.Sequence.ViennaRNA.Internal.RNALike
- CodonOptimization
- Sequence
- Tools
Downloads
- cobot-tools-0.1.2.3.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
For package maintainers and hackage trustees
Candidates
- No Candidates
| Versions [RSS] | 0.1.0.1, 0.1.1.0, 0.1.2.0, 0.1.2.1, 0.1.2.2, 0.1.2.3 |
|---|---|
| Change log | ChangeLog.md |
| Dependencies | array (>=0.5 && <0.6), base (>=4.7 && <5), bytestring, cobot, containers (>=0.5.7.1 && <0.7), data-default, data-msgpack (>=0.0.9 && <0.1), deepseq (>=1.4 && <1.5), lens (>=4.16 && <5.0), mtl (>=2.2.1 && <2.3.0), regex-tdfa, text [details] |
| License | BSD-3-Clause |
| Copyright | 2018-2019, Less Wrong Bio |
| Author | Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov |
| Maintainer | pavel@yakovlev.me |
| Uploaded | by ozzzzz at 2019-12-31T08:50:23Z |
| Category | Bio |
| Home page | https://github.com/less-wrong/cobot-tools#readme |
| Bug tracker | https://github.com/less-wrong/cobot-tools/issues |
| Source repo | head: git clone https://github.com/less-wrong/cobot-tools |
| Distributions | |
| Downloads | 2197 total (24 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs not available [build log] All reported builds failed as of 2019-12-31 [all 3 reports] |
Readme for cobot-tools-0.1.2.3
[back to package description]cobot-tools
Tools for computational biology
Software required to use cobot-tools
ViennaRNA
ViennaRNA is a library that already contains lots of useful algorithms that work with RNA sequences. We use it in order to make tools from cobot-tools better.
Installation guide for Linux can be found here.
Some issues occur when you try to install ViennaRNA for MacOS. If you want to avoid them, use the following guide.
Installation of ViennaRNA for MacOS
Installation of ViennaRNA for MacOS can be done in following steps:
- Download library. Here is the link for version 2.4.13.
- Unpack it.
- Go to the directory, where archive has been unpacked.
- Run command
./configure --without-perl --without-python. - Remove field
libRNA_la_LDFLAGSand flag-staticfrom the filesrc/ViennaRNA/Makefile.am. - Due to us having changed .am-file, it is needed to install following packages: autoconf and automake. In order to do it, run command:
brew install autoconf automake. - Run in the root of library command
autoreconf. - Compile library using command
make -j8(j8- flag that allows us to compile code using 8 jobs). - Run command
make install.
Tools of cobot-tools
Sequence.Primer.Optimisation.designPrimer
Given 'DNA' sequence and position in that sequence designs forward primer for that sequence. Primer will start at the given position.