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 __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'
