tothpetroczylab issueshttps://git.mpi-cbg.de/groups/tothpetroczylab/-/issues2024-03-25T18:54:23Zhttps://git.mpi-cbg.de/tothpetroczylab/shark/-/issues/4Generic read_fasta function2024-03-25T18:54:23ZSoumyadeep GhoshGeneric read_fasta functionThe `read_fasta_file` function in `utils` needs to be generalised so as to accept fasta text as an input as well.
This would help reuse the same function in shark-webThe `read_fasta_file` function in `utils` needs to be generalised so as to accept fasta text as an input as well.
This would help reuse the same function in shark-webSoumyadeep GhoshSoumyadeep Ghoshhttps://git.mpi-cbg.de/tothpetroczylab/shark/-/issues/3Setup coverage2024-03-25T18:53:05ZSoumyadeep GhoshSetup coveragehttps://git.mpi-cbg.de/tothpetroczylab/picnic/-/issues/5The STRIDE execution step is skipped if no AlphaFold model file (.pdb extensi...2024-03-27T13:16:25ZscheremeThe STRIDE execution step is skipped if no AlphaFold model file (.pdb extension) can be found**How to reproduce? Observed behaviour**
STRIDE is only executed if AlphaFold model file (.pdb extension) can be found! Therefore Picnic only uses features from the sequence, which is ok, but we can not guarantee the accuracy. Please ha...**How to reproduce? Observed behaviour**
STRIDE is only executed if AlphaFold model file (.pdb extension) can be found! Therefore Picnic only uses features from the sequence, which is ok, but we can not guarantee the accuracy. Please have a look at the following method.
def produce_stride_output_af(af_models_path, name, stride_out_path):
forstride = os.listdir(af_models_path)
result = [i for i in forstride if (i.startswith("AF-" + name + "-") and i.endswith(".pdb"))]
for f in result:
if f.endswith(".pdb"):
pr.execSTRIDE(af_models_path + f, outputname=f, outputdir=stride_out_path)
return
**Expected behaviour**
Exit with an appropiated error if no AlphaFold model file can be found in manual mode
cc: @soumyadeep.ghosh.consulting @hadarovi @tothpetFirst stable releasescheremescheremehttps://git.mpi-cbg.de/tothpetroczylab/shark/-/issues/1Version release workflow2024-02-13T19:06:33ZSoumyadeep GhoshVersion release workflow## Description and goal
Each release from `develop` to `master` should generate a new version of Shark along with release notes.
A release will also trigger a version release in PyPI
## Tasks and activities
* [ ] PyPI account
* [ ] D...## Description and goal
Each release from `develop` to `master` should generate a new version of Shark along with release notes.
A release will also trigger a version release in PyPI
## Tasks and activities
* [ ] PyPI account
* [ ] Directory Organisation
* [ ] setup.py
## Acceptance criteriahttps://git.mpi-cbg.de/tothpetroczylab/picnic/-/issues/4Catboost 1.2.2 installation error in python 3.122024-03-27T13:16:08ZscheremeCatboost 1.2.2 installation error in python 3.12Once a new release has been made for catboost including the Python 3.12 fix, then we can add official support of PICNIC for Python version 3.12.
reference: https://github.com/catboost/catboost/issues/2520
catboost fix: https://github.co...Once a new release has been made for catboost including the Python 3.12 fix, then we can add official support of PICNIC for Python version 3.12.
reference: https://github.com/catboost/catboost/issues/2520
catboost fix: https://github.com/catboost/catboost/commit/4bc7541199120ebc59c4bba8e1accecb57f92e89
cc: @hadaroviFirst stable releasescheremescheremehttps://git.mpi-cbg.de/tothpetroczylab/picnic/-/issues/3Implement new feature importance output function2024-03-27T13:16:18ZscheremeImplement new feature importance output functionAs discussed with @hadarovi, we will introduce a program option, which will allow you to write out all feature importance median values into a simple CSV output (headers included), which will be given to the user of picnic-bio. Priority ...As discussed with @hadarovi, we will introduce a program option, which will allow you to write out all feature importance median values into a simple CSV output (headers included), which will be given to the user of picnic-bio. Priority to be discussed with @tothpetFirst stable releasescheremeschereme