def _build_logodata(options):
motif_flag = False
fin = options.fin
if options.upload is None:
if fin is None:
fin = StringIO(sys.stdin.read())
else:
if fin is None:
from . import _from_URL_fileopen
fin = _from_URL_fileopen(options.upload)
else:
raise ValueError(
"error: options --fin and --upload are incompatible")
try:
# Try reading data in transfac format first.
from corebio.matrix import Motif
motif = Motif.read_transfac(fin, alphabet=options.alphabet)
motif_flag = True
except ValueError as motif_err:
# Failed reading Motif, try reading as multiple sequence data.
if options.input_parser == "transfac":
raise motif_err # Adding transfac as str insted of parser is a bit of a ugly kludge
seqs = read_seq_data(fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case=options.ignore_lower_case)
if motif_flag:
if options.ignore_lower_case:
raise ValueError(
"error: option --ignore-lower-case incompatible with matrix input"
)
if options.reverse or options.revcomp:
motif.reverse()
if options.complement or options.revcomp:
motif.complement()
prior = parse_prior(options.composition, motif.alphabet,
options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
else:
if options.reverse or options.revcomp:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement or options.revcomp:
if not nucleic_alphabet.alphabetic(seqs.alphabet):
raise ValueError('non-nucleic sequence cannot be complemented')
aaa = seqs.alphabet
seqs.alphabet = nucleic_alphabet
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs],
seqs.alphabet)
seqs.alphabet = aaa
prior = parse_prior(options.composition, seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
return data
def _build_logodata(options):
motif_flag = False
fin = options.fin
if options.upload is None:
if fin is None:
fin = StringIO(sys.stdin.read())
else:
if fin is None:
from . import _from_URL_fileopen
fin = _from_URL_fileopen(options.upload)
else:
raise ValueError("error: options --fin and --upload are incompatible")
try:
# Try reading data in transfac format first.
from corebio.matrix import Motif
motif = Motif.read_transfac(fin, alphabet=options.alphabet)
motif_flag = True
except ValueError as motif_err:
# Failed reading Motif, try reading as multiple sequence data.
if options.input_parser == "transfac":
raise motif_err # Adding transfac as str insted of parser is a bit of a ugly kludge
seqs = read_seq_data(fin,
options.input_parser.read,
alphabet=options.alphabet,
ignore_lower_case=options.ignore_lower_case)
if motif_flag:
if options.ignore_lower_case:
raise ValueError("error: option --ignore-lower-case incompatible with matrix input")
if options.reverse or options.revcomp:
motif.reverse()
if options.complement or options.revcomp:
motif.complement()
prior = parse_prior(options.composition, motif.alphabet, options.weight)
data = LogoData.from_counts(motif.alphabet, motif, prior)
else:
if options.reverse or options.revcomp:
seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet)
if options.complement or options.revcomp:
if not nucleic_alphabet.alphabetic(seqs.alphabet):
raise ValueError('non-nucleic sequence cannot be complemented')
aaa = seqs.alphabet
seqs.alphabet = nucleic_alphabet
seqs = SeqList([Seq(s, seqs.alphabet).complement() for s in seqs], seqs.alphabet)
seqs.alphabet = aaa
prior = parse_prior(options.composition, seqs.alphabet, options.weight)
data = LogoData.from_seqs(seqs, prior)
return data