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 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)
