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polish_carveme.py for package #24

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Tracked by #58
famosab opened this issue Oct 18, 2022 · 1 comment
Closed
Tracked by #58

polish_carveme.py for package #24

famosab opened this issue Oct 18, 2022 · 1 comment
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Refactor as Pytho...

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@famosab
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famosab commented Oct 18, 2022 •
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Determine functionality for usage within the Python package refineGEMs.
@famosab famosab added this to the Refactor as Python package milestone Oct 18, 2022
famosab added a commit that referenced this issue Nov 3, 2022
@famosab
rename to polish and add function for non-bigg models #24
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famosab commented Nov 3, 2022

Added two "main" functions. polish_not_bigg can be used for models without BiGG identifiers (as discussed in #36 ). polish_carveme_bigg is the main function that is also used in the main.py script.

@famosab famosab closed this as completed Nov 3, 2022
@famosab famosab mentioned this issue Nov 4, 2022
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GwennyGit added a commit that referenced this issue Nov 17, 2022
@GwennyGit
Generalised add_bigg_metab & add_bigg_reac #24 #36
aa67a80 
Renamed add_bigg_metab and add_bigg_reac to add_metab and add_reac and generalised the code.
GwennyGit added a commit that referenced this issue Dec 12, 2022
@GwennyGit
Changed cv_ncbiprotein function #24
7f9d181 
To better handle the annotations of the GeneProducts with the IDs contained in the model GeneProduct ID strings added by CarveMe, the function cv_ncbiprotein was adjusted. However, the ID string has to contain 'prot_' now before the actual ID. Additionally, a function to parse the input fastA file from CarveMe to add names and labels/ locus tags for IDs that are not valid ncbiprotein IDs was added.
GwennyGit added a commit that referenced this issue Dec 12, 2022
@GwennyGit
main.py & config.yml were adjusted to work with the new function in '…
48e800b 
…polish' #24
GwennyGit added a commit that referenced this issue Jan 19, 2023
@GwennyGit
Readjusted polish.py #24
da8bf35 
Now the user can specify to use the locus_tags from the CarveMe input file.
GwennyGit added a commit that referenced this issue Jan 19, 2023
@GwennyGit
Updated main.py due to changes in polish module #24
c97534a
GwennyGit added a commit that referenced this issue Jan 19, 2023
@GwennyGit
Updated config.yaml due to changes in polish module #24
bb1c8f7
@GwennyGit GwennyGit mentioned this issue Jan 31, 2023
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