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_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)
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)
def read_fastq_sequences(filename):
"""
Function to parse text from the given FASTQ file into a screed database
"""
# Will raise an exception if the file doesn't exist
theFile = open(filename, 'rb')
# Setup the iterator function
iterfunc = fastq.fastq_iter(theFile)
# Create the screed db
create_db(filename, fastq.FieldTypes, iterfunc)
theFile.close()
return ScreedDB(filename)
