From d74f461a4d799e57644ac49fac5ab1430685bf1e Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Mon, 14 Apr 2014 12:23:16 -0400
Subject: remove kmer.py

---
 kmer.py | 51 ---------------------------------------------------
 1 file changed, 51 deletions(-)
 delete mode 100644 kmer.py

(limited to 'kmer.py')

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 
-
-- 
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