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authorCalvin Morrison <mutantturkey@gmail.com>2014-04-14 12:23:16 -0400
committerCalvin Morrison <mutantturkey@gmail.com>2014-04-14 12:23:16 -0400
commitd74f461a4d799e57644ac49fac5ab1430685bf1e (patch)
tree2aad1a710e8acf4189961f7c7bc7fbe5260d93e1
parent78cd5727089714b8a6ce62a90f281a2a4106977f (diff)
remove kmer.py
-rw-r--r--kmer.py51
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
-