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#!/usr/bin/env python
params = {
'fasta': 'examples/surfg/AE004092.fasta',
'out_dir': '',
'csv': 'examples/surfg/AE004092.csv',
'protocol': 'gram_pos',
'signalp4_bin': 'signalp',
'signalp4_organism': 'gram+',
'lipop1_bin': 'LipoP',
'tmhmm_bin': 'tmhmm',
'helix_programs': ['tmhmm'],
'memsat3_bin': 'runmemsat',
'hmmsearch3_bin': 'hmmsearch',
'hmm_profiles_dir': 'protocols/gram_pos_profiles',
'hmm_evalue_max': 0.1,
'hmm_score_min': 10,
'terminal_exposed_loop_min': 50,
'internal_exposed_loop_min': 100,
}
import inmembrane
inmembrane.process(params)