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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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[Feature request] Misspeling Issue, FBA functions options #80

Open jplfaria opened 12 years ago

jplfaria commented 12 years ago

As you can see by the 3 examples bellow, due to misspell issues I am getting growth... the correct case is the 3rd one and as you guys can see no growth is observed.

Could a check for misspelling be implemented and return an error message?

[jplfaria@biologin-4 bin]$ ./fbacheckgrowth -model iJR904.24902 -media Carbon-D-Glucose -options thermo:themoerror Creating the model file: /vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400782/iJR904.24902.tbl Creating biochemistry provenance files mkdir: cannot create directory `/vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400782/MFAOutput': File exists iJR904.24902 grew in Carbon-D-Glucose media with rate:0.472273 gm biomass/gm CDW hr.

[jplfaria@biologin-4 bin]$ ./fbacheckgrowth -model iJR904.24902 -media Carbon-D-Glucose -options thermo:thermoerror Creating the model file: /vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400792/iJR904.24902.tbl Creating biochemistry provenance files mkdir: cannot create directory `/vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400792/MFAOutput': File exists iJR904.24902 grew in Carbon-D-Glucose media with rate:0.472273 gm biomass/gm CDW hr.

[jplfaria@biologin-4 bin]$ ./fbacheckgrowth -model iJR904.24902 -media Carbon-D-Glucose -options thermo;thermoerror Creating the model file: /vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400802/iJR904.24902.tbl Creating biochemistry provenance files mkdir: cannot create directory `/vol/model-dev/MODEL_DEV_DB/ReactionDB/MFAToolkitOutputFiles/2400802/MFAOutput': File exists IBM ILOG License Manager: "IBM ILOG Optimization Suite for Academic Initiative" is accessing CPLEX 12 with option(s): "e m b q ". iJR904.24902 failed to grow in Carbon-D-Glucose media. Biomass compounds cpd00119,cpd15654,cpd00062,cpd00345,cpd00107,cpd00357,cpd00129,cpd00051,cpd00023,cpd00264,cpd00356,cpd00041,cpd00052,cpd00039,cpd00026,cpd00118,cpd00053 could not be generated!

devoid commented 12 years ago

The issue is that you pass in an invalid option? And the solver does nothing if it doesn't know how to handle an option? Not sure I understand the problem.

jplfaria commented 12 years ago

yes. If you type in a wrong option the solver does nothing. and some user might think the feature is not working. there should be a warning for when you type in a wrong option. Its easy to misspell an option name.

Jose

On Wed, May 23, 2012 at 11:55 AM, Scott Devoid < reply@reply.github.com

wrote:

The issue is that you pass in an invalid option? And the solver does nothing if it doesn't know how to handle an option? Not sure I understand the problem.

Reply to this email directly or view it on GitHub: https://github.com/ModelSEED/Model-SEED-core/issues/80#issuecomment-5878317