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Try Pyrodigal as a faster and maintained Prodigal alternative #149

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oschwengers opened this issue Sep 23, 2022 · 0 comments · Fixed by #165
Closed

Try Pyrodigal as a faster and maintained Prodigal alternative #149

oschwengers opened this issue Sep 23, 2022 · 0 comments · Fixed by #165
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@oschwengers
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enhancement New feature or request
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v1.6.0

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@oschwengers
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Let's try if Pyrodigal might be a suitable, faster and most important actively maintained successor to Prodigal.
@oschwengers oschwengers added the enhancement New feature or request label Sep 23, 2022
@oschwengers oschwengers added this to the v1.6.0 milestone Sep 23, 2022
@oschwengers oschwengers self-assigned this Sep 23, 2022
oschwengers added a commit that referenced this issue Sep 23, 2022
@oschwengers
add pyrodigal dependencies #149
514cc4f
oschwengers added a commit that referenced this issue Sep 23, 2022
@oschwengers
replace Prodigal by Pyrodigal #149
e643c67
oschwengers added a commit that referenced this issue Sep 23, 2022
@oschwengers
replace Prodigal by Pyrodigal #149
20600ac
oschwengers added a commit that referenced this issue Sep 23, 2022
@oschwengers
remove check for Prodigal binary #149
08a7b45
oschwengers added a commit that referenced this issue Sep 23, 2022
@oschwengers
refactor pyrodigal training file logic #149
1521d25
oschwengers added a commit that referenced this issue Sep 27, 2022
@oschwengers
increase meta mode genome size limit to 100k #149
15f5d0d
oschwengers added a commit that referenced this issue Sep 27, 2022
@oschwengers
adopt ci tests to new CDS count #149
b38fe4c
oschwengers added a commit that referenced this issue Nov 2, 2022
@oschwengers
bump pyrodigal dependency to 2.0.2 #149
cc258a9
oschwengers added a commit that referenced this issue Nov 2, 2022
@oschwengers
fix closed parameter for circular seqs #149
f52f6ad
oschwengers added a commit that referenced this issue Nov 2, 2022
@oschwengers
remove redundant topology check for edge genes #149
284218a
oschwengers added a commit that referenced this issue Nov 2, 2022
@oschwengers
decrease of meta mode genome size to 20 kbp #149
1ae5f25
oschwengers added a commit that referenced this issue Nov 2, 2022
@oschwengers
revert CI test CDS count due to Pyrodigal 2.0 #149
0ebd468
@oschwengers oschwengers mentioned this issue Nov 3, 2022
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oschwengers added a commit that referenced this issue Nov 3, 2022
@oschwengers
update readme #149
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@oschwengers oschwengers linked a pull request Nov 3, 2022 that will close this issue
Use Pyrodigal as a faster and maintained Prodigal alternative #165
Merged
oschwengers added a commit that referenced this issue Nov 3, 2022
@oschwengers
replace Prodigal by Pyrodigal as a faster and maintained alternative (#…
93c842b 
…165)

* add pyrodigal dependencies #149
* replace Prodigal by Pyrodigal #149
* remove check for Prodigal binary #149
* refactor pyrodigal training file logic #149
* bump pyrodigal dependency to 2.0.2 #149
* fix closed parameter for circular seqs #149
* remove redundant topology check for edge genes #149
* update readme #149
@gbouras13 gbouras13 mentioned this issue Nov 29, 2022
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enhancement New feature or request
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Use Pyrodigal as a faster and maintained Prodigal alternative oschwengers/bakta
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