Comments (7)
Mentioning csv in the help is confusing, I see. Input csv should contain a peptide per line. I have added example_input.csv
and the corresponding output csv to the repo.
from hmmhc.
Thanks! That's helpful.
from hmmhc.
Thanks, I got the below error with csv as input (~150K peptides):
Traceback (most recent call last):
File "/home/dz33/.conda/envs/hmmhc/bin/hmmhc-predict", line 8, in <module>
sys.exit(main())
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/cmdline.py", line 53, in main
predictions = predictor.predict(peptides)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/hmmhc.py", line 70, in predict
normalizedLogOdds = self.computeLogOdds(peptidesList)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/hmmhc.py", line 103, in computeLogOdds
sequenceSetBlocks = self.toSequenceSetBlocks(peptideList)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/hmmhc.py", line 156, in toSequenceSetBlocks
[list(p) for p in peptideList[rangeStart:rangeEnd]]
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/ghmm.py", line 948, in __init__
internalInput = [self.emissionDomain.internalSequence(seq) for seq in sequenceSetInput]
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/ghmm.py", line 393, in internalSequence
result = map(lambda i: self.index[i], result)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/ghmm.py", line 393, in <lambda>
result = map(lambda i: self.index[i], result)
KeyError: 'X'
Some suggestions?
from hmmhc.
At least one of your peptide-encoding strings contains character 'X' which denotes an unknown amino acid and is not supported by the predictor. 'U' is also not supported.
As a quick solution, for now please input only the peptide strings containing the 20 amino acids ACDEFGHIKLMNPQRSTVWY.
We will consider filtering the peptides with unsupported amino acids in the tool itself.
from hmmhc.
I removed all peptides contains X and U but still got error
Traceback (most recent call last):
File "/home/dz33/.conda/envs/hmmhc/bin/hmmhc-predict", line 8, in <module>
sys.exit(main())
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/cmdline.py", line 53, in main
predictions = predictor.predict(peptides)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/hmmhc.py", line 70, in predict
normalizedLogOdds = self.computeLogOdds(peptidesList)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/hmmhc.py", line 103, in computeLogOdds
sequenceSetBlocks = self.toSequenceSetBlocks(peptideList)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/hmmhc/hmmhc.py", line 156, in toSequenceSetBlocks
[list(p) for p in peptideList[rangeStart:rangeEnd]]
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/ghmm.py", line 948, in __init__
internalInput = [self.emissionDomain.internalSequence(seq) for seq in sequenceSetInput]
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/ghmm.py", line 393, in internalSequence
result = map(lambda i: self.index[i], result)
File "/home/dz33/.conda/envs/hmmhc/lib/python2.7/site-packages/ghmm.py", line 393, in <lambda>
result = map(lambda i: self.index[i], result)
KeyError: '*'
from hmmhc.
As said, peptide strings shall only contain the 20 canonical amino acids. You have '*' (it usually denotes a stop codon) in at least one of the strings.
from hmmhc.
A stop codon in peptide? These are peptides from genes CDS though and I have removed all X/U letters.
from hmmhc.
Related Issues (5)
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 hmmhc.