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Applying an Application Controller Directly
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[~]|14> from cogent.app.rdp_classifier import RdpClassifier
[~]|15> rdp = RdpClassifier()
[~]|16> rdp_result = rdp(open('/Users/caporaso/projects/aln_size_tests/10_seq.fasta').read())
[~]|17> rdp.BaseCommand
[~]|19> rdp = RdpClassifier(HALT_EXEC=True)
[~]|20> rdp_result = rdp(open('/Users/caporaso/projects/aln_size_tests/10_seq.fasta').read())


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Applying an Application Controller via a Convenience Function
=============================================================

[~]|21> from cogent.app.rdp_classifier import assign_taxonomy
[~]|22> tax = assign_taxonomy(open('/Users/caporaso/projects/aln_size_tests/10_seq.fasta'))
[~]|24> tax

[~]|26> tax = assign_taxonomy(open('/Users/caporaso/projects/aln_size_tests/10_seq.fasta'),min_confidence=0.50)
[~]|27> tax


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Applying an Application Controller via command line
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caporaso@mentat ~> python ~/repo/pycogent/cogent/app/rdp_classifier.py -h
caporaso@mentat ~> python ~/repo/pycogent/cogent/app/rdp_classifier.py -c 0.50 -o tax.txt ~/projects/aln_size_tests/10_seq.fasta 
caporaso@mentat ~> cat tax.txt