# 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)
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)