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The first line from the reaction table (generated by ms bio printdbfiles [my-biochemistry] on the default biochemistry) looks different from the rest - the abbreviation is cut off and the rest of the …
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So my code is successful in merging the compounds, and I tested this extensively.
What the problem seems to be is that when the reactions themselves are added to the new biochemistry object, the comp…
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Help for this command claims that there is a verbose option for listing:
$ ms list mapping -h
$ ms list [options] ref
-v --verbose Print out additional information about the object,
…
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A minor issue - the configuration complains if MFATK_BIN is not set:
MFATK_BIN configuration is undefined!
This is the directory that contains the mfatoolkit binary. If it
is not already installed, t…
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I just ran
```
ms list biochemistry/Current_MS_Biochem
```
and got:
```
Invalid Reference at /Users/seaver/Software/ModelSEED/lib/ModelSEED/Reference.pm line 249.
```
I understood the error strai…
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At the start of https://github.com/ModelSEED/ModelSEED/wiki/Object-Definitions is a description explaining how to create objects, and indicates how to change fields within an object, but nowhere can I…
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I'm getting this message every time I run MS now:
Use of implicit split to @_ is deprecated at /Users/seaver/Software/ModelSEED/lib/ModelSEED/App/Helpers.pm line 56.
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Can someone build ModelSEED with perl 5.8 and run the tests to confirm that things are working?
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I have these cases where I basically need to copy a reaction, but change one of the compounds. I can't really use updateLinks() in this case because I'm not changing the uuid of the compounds themsel…
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Some of the functionality for an object, such as MS::Compound is found in MS::DB::Compound and MS::BaseObject etc. For any given MS Object, could I get a list of places to look for functions that app…