def sa_composition(self, num_segments, feature_ids=False):
alph = sequtil.sa_alph
if not(feature_ids):
seq = self.sa_sequence
if(num_segments == 1):
return sequtil.letter_composition(seq, alph)
else:
seqs = sequtil.segment(seq, num_segments)
return numpy.concatenate(
[sequtil.letter_composition(s, alph) for s in seqs])
else:
feat_ids = []
feat_names = []
for si in xrange(1, num_segments + 1):
for sa_id, sa_name in zip(alph, sequtil.sa_name):
feat_ids.append('%s%i' % (sa_id, si))
feat_names.append('%s, segment %i' % (sa_name, si))
return (feat_ids, feat_names)
def sa_composition(self, num_segments, feature_ids=False):
alph = sequtil.sa_alph
if not (feature_ids):
seq = self.sa_sequence
if (num_segments == 1):
return sequtil.letter_composition(seq, alph)
else:
seqs = sequtil.segment(seq, num_segments)
return numpy.concatenate(
[sequtil.letter_composition(s, alph) for s in seqs])
else:
feat_ids = []
feat_names = []
for si in xrange(1, num_segments + 1):
for sa_id, sa_name in zip(alph, sequtil.sa_name):
feat_ids.append('%s%i' % (sa_id, si))
feat_names.append('%s, segment %i' % (sa_name, si))
return (feat_ids, feat_names)
def amino_acid_composition(self, num_segments, feature_ids=False):
alph = sequtil.aa_unambiguous_alph
if not(feature_ids):
seq = self.protein_sequence
if(num_segments == 1):
return sequtil.letter_composition(seq, alph)
else:
seqs = sequtil.segment(seq, num_segments)
return numpy.concatenate(
[sequtil.letter_composition(s, alph) for s in seqs])
else:
feat_ids = []
feat_names = []
for si in xrange(1, num_segments + 1):
for aa in alph:
feat_ids.append('%s%i' % (aa, si))
feat_names.append('%s, segment %i' % (aa, si))
return (feat_ids, feat_names)
def amino_acid_composition(self, num_segments, feature_ids=False):
alph = sequtil.aa_unambiguous_alph
if not (feature_ids):
seq = self.protein_sequence
if (num_segments == 1):
return sequtil.letter_composition(seq, alph)
else:
seqs = sequtil.segment(seq, num_segments)
return numpy.concatenate(
[sequtil.letter_composition(s, alph) for s in seqs])
else:
feat_ids = []
feat_names = []
for si in xrange(1, num_segments + 1):
for aa in alph:
feat_ids.append('%s%i' % (aa, si))
feat_names.append('%s, segment %i' % (aa, si))
return (feat_ids, feat_names)
