List of all members.
Detailed Description
App-derived class for GenBank file manipulation
Member Function Documentation
| def MGT::Proj::GbFeatApp::GbFeatApp::delDbSql |
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Call this to free a connection to SQL server if it will not be needed for extended period of time
| def MGT::Proj::GbFeatApp::GbFeatApp::doWork |
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kw |
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Do the actual work.
Must be redefined in the derived classes.
Should not be called directly by the user except from doWork() in a derived class.
Should work with empty keyword dict, using only self.opt.
If doing batch submision of other App instances, must return a list of sink (final) BatchJob objects.
Reimplemented from MGT::App::App.
| def MGT::Proj::GbFeatApp::GbFeatApp::getDbSql |
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Allocate (if necessary) and return a connection to SQL server
| def MGT::Proj::GbFeatApp::GbFeatApp::initWork |
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kw |
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Perform common initialization right before doing the actual work in doWork().
Must be redefined in the derived classes.
Should not be called directly by the user except from initWork() in a derived class.
This one can create large objects because they are not passed through the batch submission,
but immediately used within the same process.
Reimplemented from MGT::App::App.
| def MGT::Proj::GbFeatApp::GbFeatApp::makeFeat |
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Create feature vectors out of FASTA files.
| def MGT::Proj::GbFeatApp::GbFeatApp::parseCmdLinePost |
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klass, |
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options, |
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args, |
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parser |
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Optionally modify options and args in-place.
Called at the end of parseCmdLine to allow the derived classes customizing the option processing.
@param options options returned by OptionParser and converted to Struct object
@param args args returned by OptionParser
@param parser OptionParser object used to parse the command line - needed here to call its error() method
if necessary.
options should be modified in place by this method
Reimplemented from MGT::App::App.
| def MGT::Proj::GbFeatApp::GbFeatApp::splitAllGenBankCds |
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self ) |
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Run splitGenBankCds for all files of a given type.
The documentation for this class was generated from the following file:
- mgtaxa/MGT/Proj/GbFeatApp.py
