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Add signal peptide predictions #32

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oschwengers opened this issue Dec 3, 2020 · 1 comment
Closed

Add signal peptide predictions #32

oschwengers opened this issue Dec 3, 2020 · 1 comment
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@Anna-Rehm
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feature
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v1.3.0

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@oschwengers
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oschwengers commented Dec 3, 2020 •
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Uuse DeepSig (GPL3) to predict signal peptides and cleavage sites.
@oschwengers oschwengers added the enhancement New feature or request label Dec 3, 2020
@oschwengers oschwengers changed the title Add signap peptide predictions Add signal peptide predictions Dec 3, 2020
Anna-Rehm added a commit that referenced this issue Apr 19, 2021
@Anna-Rehm
Add signal-peptides method to CDS annotation. #32
0f7599f
Anna-Rehm added a commit that referenced this issue Apr 19, 2021
@Anna-Rehm
Add FEATURE_SIGNAL_PEPTIDE constant. #32
a9fd8e5
Anna-Rehm added a commit that referenced this issue Apr 19, 2021
@Anna-Rehm
Add signal_peptides feature. Nomenclature only for CDS right now. #32
44638d3
Anna-Rehm added a commit that referenced this issue Apr 19, 2021
@Anna-Rehm
Changed variable names to work for all sequences. #32
de8aac2
Anna-Rehm added a commit that referenced this issue Apr 20, 2021
@Anna-Rehm
Add signal-peptides method to CDS annotation. #32
dc4e927
Anna-Rehm added a commit that referenced this issue Apr 20, 2021
@Anna-Rehm
Add FEATURE_SIGNAL_PEPTIDE constant. #32
35c41f1
Anna-Rehm added a commit that referenced this issue Apr 20, 2021
@Anna-Rehm
Add signal_peptides feature. Nomenclature only for CDS right now. #32
1c45336
Anna-Rehm added a commit that referenced this issue Apr 20, 2021
@Anna-Rehm
Changed variable names to work for all sequences. #32
1616876
Anna-Rehm added a commit that referenced this issue Apr 20, 2021
@Anna-Rehm
Add sORF signal peptide analysis. #32
45fc60e
Anna-Rehm added a commit that referenced this issue Apr 20, 2021
@Anna-Rehm
Change seq to orf. #32
9d5e3f9
Anna-Rehm added a commit that referenced this issue Apr 20, 2021
@Anna-Rehm
Add test for start_stop_orf() in feature signal_peptides. #32
cf4112b
Anna-Rehm added a commit that referenced this issue Apr 21, 2021
@Anna-Rehm
Add method start_stop_orf to signal_peptides. #32
6870c21
Anna-Rehm added a commit that referenced this issue Apr 21, 2021
@Anna-Rehm
Change signal peptides from own features to CDS/sORF features. #32
aaacff8
Anna-Rehm added a commit that referenced this issue Apr 21, 2021
@Anna-Rehm
Change signal peptides from own features to CDS/sORF features in sign…
b920689 
…al_peptides.py as well. #32
Anna-Rehm added a commit that referenced this issue Apr 26, 2021
@Anna-Rehm
Fix typo feature_annotation_score. #32
9c8fb4c
Anna-Rehm added a commit that referenced this issue Apr 26, 2021
@Anna-Rehm
Add signal_peptide export. #32
c6ddb84
Anna-Rehm added a commit that referenced this issue May 4, 2021
@Anna-Rehm
Add signal peptide feature to CDS and sORF genbank and EMBL output. #32
9e4f2d3
Anna-Rehm added a commit that referenced this issue May 4, 2021
@Anna-Rehm
Add write_signal_peptide(). #32
9c15a2f
Anna-Rehm added a commit that referenced this issue May 4, 2021
@Anna-Rehm
Fix signal peptide to store correct start and stop positions. #32
dada349
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Change sORF signal peptide fasta file creation. #32
367dae4
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Change sig_peps to list, code refactoring. #32
d5840e6
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Fix GFF3 output for signal peptides, code refactoring. #32
fc5e76e
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Change position of accompanying_features, code refactoring. #32
dc8126d
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Fix camel case to snake case. #32
61256a9
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Add signal-peptides method to CDS annotation. #32
1f355da
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Add FEATURE_SIGNAL_PEPTIDE constant. #32
dedd785
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Add signal_peptides feature. Nomenclature only for CDS right now. #32
baee033
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Add write_signal_peptide(). #32
e83c582
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Fix signal peptide to store correct start and stop positions. #32
d1626a5
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Change sORF signal peptide fasta file creation. #32
7720775
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Change sig_peps to list, code refactoring. #32
d00a549
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Fix GFF3 output for signal peptides, code refactoring. #32
8235c53
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Change position of accompanying_features, code refactoring. #32
616ba85
Anna-Rehm added a commit that referenced this issue May 5, 2021
@Anna-Rehm
Fix camel case to snake case. #32
5b62cfc
@Anna-Rehm Anna-Rehm mentioned this issue May 5, 2021
Closed
@oschwengers oschwengers added feature and removed enhancement New feature or request labels Jun 14, 2021
oschwengers added a commit that referenced this issue Sep 7, 2021
@oschwengers
introduce signal prediction by DeepSig #32
5182276
oschwengers added a commit that referenced this issue Sep 7, 2021
@oschwengers
add DeepSig dependency check #32
9c461e8
@oschwengers oschwengers added this to the v1.3.0 milestone Jan 4, 2022
@oschwengers oschwengers mentioned this issue Jan 11, 2022
Closed
oschwengers added a commit that referenced this issue Jan 17, 2022
@oschwengers
add deepsig dependency #32
8d04eb3
oschwengers added a commit that referenced this issue Jan 17, 2022
@oschwengers
add signal peptide tests #32
74edaef
oschwengers added a commit that referenced this issue Jan 17, 2022
@oschwengers
add signal peptide annotation #32
d161ca4
@oschwengers oschwengers mentioned this issue Jan 17, 2022
Merged
oschwengers added a commit that referenced this issue Jan 18, 2022
@oschwengers
fix signal peptide score log #32
39eb244
oschwengers added a commit that referenced this issue Jan 18, 2022
@oschwengers
add signal peptides to output #32
4f8e23b
oschwengers added a commit that referenced this issue Jan 19, 2022
@oschwengers
polish readme #32
6ea1019
oschwengers added a commit that referenced this issue Jan 19, 2022
@oschwengers
exclude DeepSig from Conda dependencies #32
d4cb86a
oschwengers added a commit that referenced this issue Jan 19, 2022
@oschwengers
include DeepSig in CI tests on Linux #32
06ab058
oschwengers added a commit that referenced this issue Jan 20, 2022
@oschwengers
add DeepSig in Dockerfile #32
a178a97
oschwengers added a commit that referenced this issue Jan 20, 2022
@oschwengers
expand CI to Python 3.8 & 3.9 #32
0e68498
oschwengers added a commit that referenced this issue Jan 20, 2022
@oschwengers
remove Python 3.9 from CI until DeepSig is available #32
5fa46fc
oschwengers added a commit that referenced this issue Jan 20, 2022
@oschwengers
amend sig pep skip msg #32
dcbeb30
@oschwengers
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We'd like to expand CI tests to Python versions 3.8 and 3.9. However, we had to remove 3.9 from CI tests due to TensorFlow und Keras dependency restrictions that are not available for Python > 3.8.

This is fixed by BolognaBiocomp/deepsig#30

oschwengers added a commit that referenced this issue Jan 20, 2022
@oschwengers
Add signal peptide predictions (#91)
aa552c0 
* add deepsig dependency #32
* add signal peptide tests #32
* add signal peptide annotation #32
* rename orf aa path var
* fix signal peptide score log #32
* add signal peptides to output #32
* polish readme #32
* exclude DeepSig from Conda dependencies #32
* include DeepSig in CI tests on Linux #32
* add DeepSig in Dockerfile #32
* expand CI to Python 3.8 & 3.9 #32
* remove Python 3.9 from CI until DeepSig is available #32
* update readme
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