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| -rw-r--r-- | kmer.py | 51 |
1 files changed, 0 insertions, 51 deletions
diff --git a/kmer.py b/kmer.py deleted file mode 100644 index 1774f5f..0000000 --- a/kmer.py +++ /dev/null @@ -1,51 +0,0 @@ -''' - -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 get_counts_from_file(fn, kmer): - ''' - load kmer counts from a filename (not a handle), of size kmer. - -returns an array size 4^k of counts - - >>> import kmer - >>> counts = kmer.get_counts_from_file("test.fa", 6) - - ''' - - if type(fn) is not str: - raise TypeError("fn must be a str"); - if type(kmer) is not int: - raise TypeError("fn must be int"); - - ret = [] - width = (kmer ** 4) - libkmer.get_kmer_counts_from_filename.restype = c.POINTER(c.c_ulonglong * width ) - counts = libkmer.get_kmer_counts_from_filename(fn, kmer); - - if counts: - for i in counts.contents: - ret.append(i) - else: - ret = 'error could not count mers on' + str(fn) - - return ret - |