Comments (3)
dear @valentin994 it's great that you found the code useful. Let me know if you need any help.
And yeah, let me see what you have so we can improve the package here.
from rna-tools.
In the end, I ended up creating a parser, it might be useful here too, or biopython so let me know what you think.
So the problem I stumbled upon when using RnaStructure().get_sequence
is that I wouldn't always get the sequence expected (I can't really explain in biological terms as I'm a developer but I'll run through examples that might give you insight onto this).
For example these pdb files "2l8h", "6b14", "6las" the output from get_sequence()
would be:
- GGCAGAUCUGAGCCUGGGAGCUCUCUGCCRh
- GACGCGACCGAAAUGGUGAAGGACGGGUCCAGUGCGAAACACGCACUGUUGAGUAGAGUGUGAGCUCCGUAACUGGUCGCGUCghhhhhhhhhhhhhhhhhhhhhhhhh
- GUUGAUAUGGAUUUACUCCGAGGAGACGAACUACCACGAACAGGGGAAACUCUACCCGUGGCGUCUCCGUUUGACGAGUAAGUCCUAAGUCAACAggggooooghhhhhhhh
- GGCAUUGUGCCUCGCAUUGCACUCCGCGGGGCGAUAAGUCCUGAAAAGGGAUGUCmhhhhhhhhh GGCAUUGUGCCUCGCAUUGCACUCCGCGGGGCGAUAAGUCCUGAAAAGGGAUGUChh RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVKRSLKeRGQAFVIFKEVSSATNALRSeQGFPFYDKPeRIQYAKTDSDIIAKehh TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVKRSLKeRGQAFVIFKEVSSATNALRSeQGFPFYDKPeRIQYAKTDSDIIAKeAhhhhh RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVKRSLKeRGQAFVIFKEVSSATNALRSeQGFPFYDKPeRIQYAKTDSDIhhhh
While I would expect:
- GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
- GACGCGACCGAAAUGGUGAAGGACGGGUCCAGUGCGAAACACGCACUGUUGAGUAGAGUGUGAGCUCCGUAACUGGUCGCGUC
- GUUGAUAUGGAUUUACUCCGAGGAGACGAACUACCACGAACAGGGGAAACUCUACCCGUGGCGUCUCCGUUUGACGAGUAAGUCCUAAGUCAACA
- GGCAUUGUGCCUCGCAUUGCACUCCGCGGGGCGAUAAGUCCUGAAAAGGGAUGUC
The expected sequences is what you can get if you get the fasta version of the files mentioned and you pull out the sequence with SeqIo parser. Now I'm not sure if the sequences I get from this package are the expected behaviour, or if there is any need to be able to parse them out like I do now. If you find it useful I can create a PR or show you more in depth how it would look. I hope that I managed to explain it well enough 😓
from rna-tools.
Oh, I sidetracked from the original question. But yeah initializing with bytes can also be done.
from rna-tools.
Related Issues (20)
- web: better info when rmsd is not calculated
- moderna missing data if installed with pip
- clarna_app - NameError: name 'ClaRNA_play_path' is not defined
- rna_calc_inf web view HOT 2
- for VARNA vis use varnaapi
- binaries for Colab
- rna_pdb_tools.py --rpr 1ehz.pdb --replace-hetatm KeyError: "C3'" HOT 1
- --get-seq should be fasta fasta
- calc rmsd: show rmsd without pandas and any other options
- calc rmsd, target and the rest, without -t ?
- fix rpr for 1ehz [trna] HOT 1
- rna std add gaps and modified residues to output
- rna_pdb_inspect.py HOT 1
- rna_pdb_tools.py: command not found HOT 4
- --rpr function causes signififant change in the coordinates HOT 2
- rna_pdb_tools.py with fetch for given residue
- rna_pdb_tools.py with fetch cif files as well
- `rna_pdb_tools.py --get-ss` causes NameError. HOT 1
- rna_pdb_tools.py -- TypeError when running --edit option HOT 2
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 rna-tools.