recs[j].seq._data[int(k):]
full_rf_table = full_rf_table_lst[j]
bp = full_rf_table.index(k)
inter_rf = []
for t in filter(lambda x: x%3==0, range(len(gaps))):
inter_rf.append(k+t+3.0)
full_rf_table = full_rf_table[:bp] + inter_rf + \
[v+int(gap_num) for v in full_rf_table[bp:]]
full_rf_table_lst[j] = full_rf_table
recs[j].seq = CodonSeq(seq,
rf_table=recs[j].seq.rf_table,
alphabet=recs[j].seq.alphabet)
i += 1
return recs
#def toCodonAlignment(align, alphabet=default_codon_alphabet):
# """Function to convert a MultipleSeqAlignment to CodonAlignment.
# It is the user's responsibility to ensure all the requirement
# needed by CodonAlignment is met.
#
# """
# rec = [SeqRecord(CodonSeq(str(i.seq), alphabet=alphabet), id=i.id) \
# for i in align._records]
# return CodonAlignment(rec, alphabet=align._alphabet)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
taxonomy = "."
self._write_multi_line("OC", taxonomy)
handle.write("XX\n")
if "references" in record.annotations:
self._write_references(record)
if "comment" in record.annotations:
self._write_comment(record)
handle.write(self.FEATURE_HEADER)
rec_length = len(record)
for feature in record.features:
self._write_feature(feature, rec_length)
handle.write("XX\n")
self._write_sequence(record)
handle.write("//\n")
class ImgtWriter(EmblWriter):
HEADER_WIDTH = 5
QUALIFIER_INDENT = 25 # Not 21 as in EMBL
QUALIFIER_INDENT_STR = "FT" + " " * (QUALIFIER_INDENT - 2)
QUALIFIER_INDENT_TMP = "FT %s " # 25 if %s is empty
FEATURE_HEADER = "FH Key Location/Qualifiers\n"
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest(verbose=0)
def int255_color(self, values):
"""Map integer (red, green, blue) tuple to a ReportLab Color object.
- values: A tuple of (red, green, blue) intensities as
integers in the range 0->255
Takes a tuple of (red, green, blue) intensity values in the range
0 -> 255 and returns an appropriate colors.Color object.
"""
red, green, blue = values
factor = 1 / 255.
red, green, blue = red * factor, green * factor, blue * factor
return colors.Color(red, green, blue)
def float1_color(self, values):
"""Map float (red, green, blue) tuple to a ReportLab Color object.
- values: A tuple of (red, green, blue) intensities as floats
in the range 0 -> 1
Takes a tuple of (red, green, blue) intensity values in the range
0 -> 1 and returns an appropriate colors.Color object.
"""
red, green, blue = values
return colors.Color(red, green, blue)
if __name__ == '__main__':
from Bio._utils import run_doctest
run_doctest(verbose=2)
"""Return a string representation of motifs in the given format.
Currently supported formats (case is ignored):
- clusterbuster: Cluster Buster position frequency matrix format
- pfm : JASPAR simple single Position Frequency Matrix
- jaspar : JASPAR multiple PFM format
- transfac : TRANSFAC like files
"""
format = format.lower()
if format in ("pfm", "jaspar"):
from Bio.motifs import jaspar
return jaspar.write(motifs, format)
elif format == "transfac":
from Bio.motifs import transfac
return transfac.write(motifs)
elif format == "clusterbuster":
from Bio.motifs import clusterbuster
return clusterbuster.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest(verbose=0)
return header
def _build_row(self, qresult):
"""Returns a string or one row or more of the QueryResult object."""
rows = ''
# calculate whitespace required
# adapted from HMMER's source: src/p7_tophits.c#L1083
qnamew = max(20, len(qresult.id))
tnamew = max(20, len(qresult[0].id))
qaccw = max(10, len(qresult.acc))
taccw = max(10, len(qresult[0].acc))
for hit in qresult:
rows += "%-*s %-*s %-*s %-*s %9.2g %6.1f %5.1f %9.2g %6.1f %5.1f " \
"%5.1f %3d %3d %3d %3d %3d %3d %3d %s\n" % (tnamew, hit.id, taccw,
hit.acc, qnamew, qresult.id, qaccw, qresult.acc, hit.evalue,
hit.bitscore, hit.bias, hit.hsps[0].evalue, hit.hsps[0].bitscore,
hit.hsps[0].bias, hit.domain_exp_num, hit.region_num, hit.cluster_num,
hit.overlap_num, hit.env_num, hit.domain_obs_num,
hit.domain_reported_num, hit.domain_included_num, hit.description)
return rows
# if not used as a module, run the doctest
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
"""Map integer (red, green, blue) tuple to a ReportLab Color object.
- values: A tuple of (red, green, blue) intensities as
integers in the range 0->255
Takes a tuple of (red, green, blue) intensity values in the range
0 -> 255 and returns an appropriate colors.Color object.
"""
red, green, blue = values
factor = 1 / 255.0
red, green, blue = red * factor, green * factor, blue * factor
return colors.Color(red, green, blue)
def float1_color(self, values):
"""Map float (red, green, blue) tuple to a ReportLab Color object.
- values: A tuple of (red, green, blue) intensities as floats
in the range 0 -> 1
Takes a tuple of (red, green, blue) intensity values in the range
0 -> 1 and returns an appropriate colors.Color object.
"""
red, green, blue = values
return colors.Color(red, green, blue)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest(verbose=2)