def __init__(self, name, sequence_centre_key_regex, threshold, phylo_threshold, directory='.'): self.name = name self.seqs = biopsy.parse_fasta(fasta_file(name)) self.converted_seqs = biopsy.analyse_remos.convert_dict_seqs_for_phylo_analysis( self.seqs, centre_key_regex=sequence_centre_key_regex) self.threshold = threshold self.phylo_threshold = phylo_threshold self.directory = directory
def test_score_fasta(): print '******** test_score_fasta()' sequences = biopsy.SequenceVec() for name, seq in biopsy.parse_fasta( 'c:/analysis/keiths/msx1/enhancerD.fa' ).iteritems(): print name, ':', len( seq ), 'bases' sequences.append( seq ) if len( sequences) >= 3: break phylo_result = biopsy.score_pssms_on_phylo_sequences( biopsy.get_transfac_pssm_accessions( biopsy.get_default_transfac_pssm_filter() ), sequences, 0.05 ) print 'Max Chain:' print phylo_result[ 1 ] # print biopsy.sort_hits_by_position( phylo_result[ 0 ] ) print 'Got', len( phylo_result[ 0 ] ), 'hits from', len( sequences[ 0 ] ), 'bases'
def test_score_fasta(): print '******** test_score_fasta()' sequences = biopsy.SequenceVec() for name, seq in biopsy.parse_fasta( 'c:/analysis/keiths/msx1/enhancerD.fa').iteritems(): print name, ':', len(seq), 'bases' sequences.append(seq) if len(sequences) >= 3: break phylo_result = biopsy.score_pssms_on_phylo_sequences( biopsy.get_transfac_pssm_accessions( biopsy.get_default_transfac_pssm_filter()), sequences, 0.05) print 'Max Chain:' print phylo_result[1] # print biopsy.sort_hits_by_position( phylo_result[ 0 ] ) print 'Got', len(phylo_result[0]), 'hits from', len(sequences[0]), 'bases'