def ToFasta(dbFile, outputFile): """ Opens the screed database file and attempts to dump it to a FASTA-formatted text file """ outFile = open(outputFile, 'wb') db = ScreedDB(dbFile) for value in db.itervalues(): ToFastaWrite(outFile, value) db.close() outFile.close()
def ToFastaRecs(dbFile, record_indices, outputFile=None, outFile=None): """Write individual records to a new FASTA-formatted file. """ if outFile is None: outFile = open(outputFile, 'wb') db = ScreedDB(dbFile) for i in record_indices: value = db.loadRecordByIndex(i) ToFastaWrite(outFile, value) db.close() if outFile is None: outFile.close()
def ToFasta(dbFile, outputFile): """ Opens the screed database file and attempts to dump it to a FASTA-formatted text file """ outFile = open(outputFile, 'wb') db = ScreedDB(dbFile) for value in db.itervalues(): outFile.write('>%s %s\n%s\n' % (value['name'], GetComments(value), linewrap(str(value['sequence'])))) db.close() outFile.close()
def read_fasta_sequences(filename): """ Function to parse text from the given FASTA file into a screed database """ import openscreed # Will raise an exception if the file doesn't exist iterfunc = openscreed.open(filename) # Create the screed db create_db(filename, fasta.FieldTypes, iterfunc) return ScreedDB(filename)
def read_hava_sequences(filename): """ Function to parse text from the given HAVA file into a screed database """ # Will raise an exception if the file doesn't exist theFile = open(filename, "rb") # Setup the iterator function iterfunc = hava.hava_iter(theFile) # Create the screed db create_db(filename, hava.FieldTypes, iterfunc) theFile.close() return ScreedDB(filename)