deepgo

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Bumps [numpy](https://github.com/numpy/numpy) from 1.15.2 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 0.12.1 to 2.7.2. Release notes Sourced from tensorflow's releases. TensorFlow 2.7.2 Release 2.7.2 This releases introduces several vulnerability fixes: Fixes a code injection in saved_model_cli (CVE-2022-29216) Fixes...

dependabot[bot]

Bumps [protobuf](https://github.com/protocolbuffers/protobuf) from 3.1.0 to 3.15.0. Release notes Sourced from protobuf's releases. Protocol Buffers v3.15.0 Protocol Compiler Optional fields for proto3 are enabled by default, and no longer require the...

dependabot[bot]

tensorflow new version

1

Which is the python version that deepgo is most suitable for ? As one of the package l tensorflow==0.12.1 wasnot supported by my python 3.7.0 and when I switched to...

dikshyantg

Bumps [pyyaml](https://github.com/yaml/pyyaml) from 3.12 to 5.4. Changelog Sourced from pyyaml's changelog. 5.4 (2021-01-19) yaml/pyyaml#407 -- Build modernization, remove distutils, fix metadata, build wheels, CI to GHA yaml/pyyaml#472 -- Fix for...

dependabot[bot]

Writing bytes parentheses issue

1

https://github.com/bio-ontology-research-group/deepgo/blob/36c3a611238c236d7e41dfd9b33d2d93ba4b5e2e/predict_all.py#L112 I think this line should be:` p.stdin.write(bytes('>' + str(i) + '\n' + sequences[i] + '\n', encoding='utf-8'))` Found this when executing dependent code and ran into type error: ``` File...

hmvantol

Hello, Thank you for your work. Is your data in the form of owl/rdf originally from the ontology?

Avv22

Protein vectors in protein-interaction-network

2

The paper cites the protein vectors in Alshahrani,M. et al. (2017). Did you use exactly the same vectors by Alshahrani,M. et al. (2017)? In this paper Alshahrani,M. et al. (2017),...

datduong

Pytorch implementation

1

I have a [Pytorch implementation](https://github.com/datduong/EncodeGeneOntology/blob/master/ProtSeq2GO/ProtSeq2GOModel.py#L440 ) for DeepGO Flat with Protein network which has been tested and produces consistent results with original Keras implementation. If you're interested, we can merge.

datduong

Update code for Python 3 (Python 2.7 no longer maintained after January 1, 2020)

2

https://pythonclock.org/ print function xrange to range many things now return iterators/generators vs. list objects. etc., etc. 2to3 script can help

bdklahn