def _build_logodata(options):
if options.input_parser != "transfac":
seqs = read_seq_data(options.fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case=options.ignore_lower_case)
if options.reverse:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement:
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs],
seqs.alphabet)
prior = parse_prior(options.composition, seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
else:
from corebio.matrix import Motif
if options.ignore_lower_case:
raise ValueError(
"error: option --ignore-lower-case incompatible with matrix input"
)
#FIXME : implement
if options.reverse:
raise ValueError(
"error: option --reverse incompatible with matrix input")
#FIXME : implement
if options.complement:
raise ValueError(
"error: option --complement incompatible with matrix input")
motif = Motif.read_transfac(options.fin, alphabet=options.alphabet)
prior = parse_prior(options.composition, motif.alphabet,
options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
return data
if options.ignore_lower_case:
raise ValueError("error: option --ignore-lower-case incompatible with matrix input")
if options.reverse: motif.reverse()
if options.complement: motif.complement()
prior = parse_prior( options.composition,motif.alphabet, options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
else :
if options.reverse:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement :
seqs= SeqList( [Seq(s,seqs.alphabet).complement() for s in seqs], seqs.alphabet)
prior = parse_prior( options.composition,seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
return data
def _build_logoformat( logodata, opts) :
""" Extract and process relevant option values and return a
LogoFormat object."""
args = {}
direct_from_opts = [
"stacks_per_line",
if options.reverse: motif.reverse()
if options.complement: motif.complement()
prior = parse_prior(options.composition, motif.alphabet,
options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
else:
if options.reverse:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement:
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs],
seqs.alphabet)
prior = parse_prior(options.composition, seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
return data
def _build_logoformat(logodata, opts):
""" Extract and process relevant option values and return a
LogoFormat object."""
args = {}
direct_from_opts = [
"stacks_per_line",
"logo_title",
"yaxis_label",
"show_xaxis",
"show_yaxis",
if options.complement:
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs], seqs.alphabet)
if isCodon:
if abs(options.codon_frame) > 1:
beg = abs(options.codon_frame) - 1
end = beg + int((len(seqs[0]) - beg) / 3) * 3
seqs = SeqList([s[beg:end] for s in seqs], seqs.alphabet)
if std_alphabets["dna"] == seqs.alphabet:
seqs.alphabet = codon_dna_alphabet
elif std_alphabets["rna"] == seqs.alphabet:
seqs.alphabet = codon_rna_alphabet
prior, compos = parse_prior(fin_compos, seqs.alphabet, fin_weight)
data = LogoData.from_seqs(seqs, options.stats_func, prior, compos, second_data)
return data
def _build_logodata(options):
if options.second_data is not None:
ngdata = _build_logodata_core(options.second_data, options.second_composition, options.second_weight, options)
fin = options.fin
if fin is None:
from StringIO import StringIO
fin = StringIO(sys.stdin.read())
if options.second_data is not None:
data = _build_logodata_core(fin, options.composition, options.weight, options, ngdata)
else:
data = _build_logodata_core(fin, options.composition, options.weight, options)
