# read header first
handle.seek(0)
while True:
line = handle.readline()
peekline = handle.peekline()
qresult_raw += line
if not peekline.startswith(query_mark) and query_mark in peekline:
break
# and read the qresult raw string
handle.seek(offset)
while True:
# preserve whitespace, don't use read_forward
line = handle.readline()
peekline = handle.peekline()
qresult_raw += line
# break when we've reached qresult end
if (not peekline.startswith(query_mark) and query_mark in peekline) or \
not line:
break
# append mock end marker to qresult_raw, since it's not always present
return qresult_raw + _as_bytes('>>><<<\n')
# if not used as a module, run the doctest
if __name__ == "__main__":
from SAP.Bio._utils import run_doctest
run_doctest()
from SAP.Bio.motifs import transfac
motifs = [self]
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
def write(motifs, format):
"""Returns a string representation of motifs in a given format
Currently supported formats (case is ignored):
- 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 SAP.Bio.motifs import jaspar
return jaspar.write(motifs, format)
elif format == "transfac":
from SAP.Bio.motifs import transfac
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
if __name__ == "__main__":
from SAP.Bio._utils import run_doctest
run_doctest(verbose=0)
# read header first
handle.seek(0)
while True:
line = handle.readline()
peekline = handle.peekline()
qresult_raw += line
if not peekline.startswith(query_mark) and query_mark in peekline:
break
# and read the qresult raw string
handle.seek(offset)
while True:
# preserve whitespace, don't use read_forward
line = handle.readline()
peekline = handle.peekline()
qresult_raw += line
# break when we've reached qresult end
if (not peekline.startswith(query_mark) and query_mark in peekline) or \
not line:
break
# append mock end marker to qresult_raw, since it's not always present
return qresult_raw + _as_bytes('>>><<<\n')
# if not used as a module, run the doctest
if __name__ == "__main__":
from SAP.Bio._utils import run_doctest
run_doctest()
else:
raise ValueError("Unknown format type %s" % format)
def write(motifs, format):
"""Returns a string representation of motifs in a given format
Currently supported formats (case is ignored):
- 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 SAP.Bio.motifs import jaspar
return jaspar.write(motifs, format)
elif format == "transfac":
from SAP.Bio.motifs import transfac
return transfac.write(motifs)
else:
raise ValueError("Unknown format type %s" % format)
if __name__ == "__main__":
from SAP.Bio._utils import run_doctest
run_doctest(verbose=0)
