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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Can't run classifyreactions #28

Closed mdejongh closed 13 years ago

mdejongh commented 13 years ago

~/Desktop/ModelSEED/Model-SEED-core/bin> ModelDriver classifyreactions?iJR904.3?Complete?0?0

Processing argument: classifyreactions?iJR904.3?Complete?0?0 Use of uninitialized value in pattern match (m//) at /Users/dejongh/Desktop/ModelSEED/Model-SEED-co\ re/lib/PPO/DBObject.pm line 495. Now processing model: iJR904.3 /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/software/mfatoolkit/bin/mfatoolkit resetparameter \ "MFA input directory" /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/ parameterfi\ le "../Parameters/ProductionMFA.txt" parameterfile "/Users/dejongh/Desktop/ModelSEED/Model-SEED-cor\ e/data/ReactionDB/MFAToolkitOutputFiles/2098263/FluxVariabilityAnalysis.txt" parameterfile "/Users/\ dejongh/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MFAToolkitOutputFiles/2098263/AddnlFBAPar\ ameters.txt" LoadCentralSystem "/Users/dejongh/Desktop/ModelSEED/Model-SEED-core/data/ReactionDB/MF\ AToolkitOutputFiles/2098263/iJR904.3.tbl" > "/Users/dejongh/Desktop/ModelSEED/Model-SEED-core/logs/\ fba-2098263.log" StringDBTable:loadFromFile:could not open table file StringDBTable:loadFromFile:could not open table file mkdir: /scratch: No such file or directory cp: /scratch/2098263: No such file or directory FIGMODELfba:parseTightBounds:could not find tight bound results file SUCCESS: FAIL:iJR904.3;

cshenry commented 13 years ago

So I decided to create a new more general function called "fbafva". This function allows you to specify a model, media condition, list of variables to be minimized and maximized, some general options, a filename for output, and flags indicating if results should be saved in the database. By default, the variables minimized and maximized are flux and uptake.

The function prints output to an excel file, although output to text remains an option. We'll be documenting in the wiki shortly.

mdejongh commented 13 years ago

Chris - what parameters/values should I use to duplicate what classifyreactions does?