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'''
The kmer module provides an interface between the C-library
for quikr kmer counting in Python
'''
__author__ = "Calvin Morrison"
__copyright__ = "Copyright 2013, EESI Laboratory"
__credits__ = ["Calvin Morrison"]
__license__ = "GPL"
__version__ = "0.1.0"
__maintainer__ = "Calvin Morrison"
__email__ = "mutantturkey@gmail.com"
__status__ = "development"
import numpy as np
import ctypes as c
try:
libkmer = c.CDLL("libkmer.so");
except:
raise Exception("Error: could not load libkmer.so")
def load_kmer_counts_from_file(fh, kmer):
'''
'''
ret = []
width = (kmer ** 4) + 1
libkmer.get_kmer_counts_from_filename.restype = c.POINTER(c.c_ulonglong * width )
counts = libkmer.get_kmer_counts_from_filename(fh, kmer);
if counts.contents:
for i in counts.contents:
ret.append(i)
else:
ret = 'error'
return ret
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