def create_analysis(
self,
pssm_names,
file_tag='',
max_threshold=0.0
):
print 'Analysing %s' % self.name
hits, max_chain, unadjusted_hits = biopsy.score_pssms_on_phylo_sequences(
pssm_names,
self.converted_seqs,
threshold = self.threshold,
phylo_threshold = self.phylo_threshold
)
notes = 'Species:\n\t%s\nThreshold: %f\nPhylo: %f' % (
"\n\t".join( self.seqs.keys() ),
self.threshold,
self.phylo_threshold
)
self.write_svg(
filename = '%s/bifa-%s%s.svg' % (self.directory, self.name, file_tag),
max_threshold = max_threshold,
notes = notes,
hits = hits,
max_chain = max_chain
)
return hits, max_chain
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'
def create_analysis(self, pssm_names, file_tag='', max_threshold=0.0):
print 'Analysing %s' % self.name
hits, max_chain, unadjusted_hits = biopsy.score_pssms_on_phylo_sequences(
pssm_names,
self.converted_seqs,
threshold=self.threshold,
phylo_threshold=self.phylo_threshold)
notes = 'Species:\n\t%s\nThreshold: %f\nPhylo: %f' % ("\n\t".join(
self.seqs.keys()), self.threshold, self.phylo_threshold)
self.write_svg(filename='%s/bifa-%s%s.svg' %
(self.directory, self.name, file_tag),
max_threshold=max_threshold,
notes=notes,
hits=hits,
max_chain=max_chain)
return hits, max_chain
