Closed nconrad closed 9 years ago
I see the problem here. This reaction came from the metabolic model iMO1053 (PA_CORE3s) and the full name of the compound is:
'Pseudomonas aeruginosa LPS core precursor 2 + KDO2-lipidA'
So the ' + ' means you're getting a parsing error, and not retrieving the full name of the compound. This occurs more than once, a quick parse gives me 25 compounds where the name itself contains a ' + ' string, such as:
'(K+ + H+)-ATPase'
I think you'll have to print the equation string using compound identifiers every time, before replacing the identifiers with the relevant names, which can be a pain, but is probably the safest way to do this. In the meantime, we can certainly consider what to do with these rogue ' + ' strings, we can simply remove the spaces so we'd get names like:
'Pseudomonas aeruginosa LPS core precursor 2+KDO2-lipidA' '(K++H+)-ATPase'
I added modifications to the compound and reaction master.mods files to adjust the names that have embedded ' + ' strings to remove the spaces as Sam suggested.
I also found 2 reactions that had an embedded ' <=> ' and I also added a modification to remove the extra spaces.
@nconrad, are you OK with the change to remove spaces? Just wondering if this issue can be closed.
Yeah, that sounds fine.
I'm on vacation until Monday. I'll address other tickets when I get back. We should regroup when I get back, if possible... And do another push on the site. I've made some progress that I haven't commited yet.
On Wednesday, August 19, 2015, Mike Mundy notifications@github.com wrote:
@nconrad https://github.com/nconrad, are you OK with the change to remove spaces? Just wondering if this issue can be closed.
— Reply to this email directly or view it on GitHub https://github.com/ModelSEED/ModelSEEDDatabase/issues/6#issuecomment-132746317 .
t. 815-508-7951 e. nealconrad@gmail.com
Should all compounds in reactions have compartments?
I see "Pseudomonas aeruginosa LPS core precursor 2" in rxn13866 doesn't:
https://www.patricbrc.org/api/model_reaction/?http_accept=application/json&eq(id,rxn13866)&select(definition)