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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py125
1 files changed, 92 insertions, 33 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index cc155ee0..db617b23 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -104,48 +104,107 @@ def run_human(pheno_vector,
def divide_into_chunks(the_list, number_chunks):
-
length = len(the_list)
- print("length the_list:", length)
-
- remainder = length % number_chunks
-
- print("remainder is:", remainder)
-
- #if remainder:
- # number_chunks -= 1
-
- chunksize = int(length / number_chunks) + 1
- print("chunksize:", chunksize)
-
- #remainder = length % number_chunks
- #assert (chunksize * number_chunks) + remainder == length, "Best check yourself!"
-
+ if length == 0:
+ return [[]]
+
+ if number_chunks > length:
+ number_chunks = length
+
+ remainder = length - (int(length / number_chunks) * number_chunks)
+ if remainder > 0:
+ chunksize = int(length / number_chunks) + 1
+ while (chunksize * number_chunks) > length:
+ number_chunks -= 1
+ else:
+ chunksize = int(length / number_chunks)
+
chunks = []
- for counter in range(0, length-1, chunksize):
- print("counter is:", counter)
+ for counter in range(0, length, chunksize):
chunks.append(the_list[counter:counter+chunksize])
- print("chunks is now:", chunks)
-
- # Deal with remainder
- #if remainder:
- # chunks.append(the_list[(counter + chunksize):])
- # Sanity check
- all_chunked = []
- for chunk in chunks:
- all_chunked.extend(chunk)
- print("length of all chunked:", len(all_chunked))
- assert the_list == all_chunked, "You didn't chunk right"
-
return chunks
+def confirm_chunk(original, result):
+ all_chunked = []
+ for chunk in result:
+ all_chunked.extend(chunk)
+ assert original == all_chunked, "You didn't chunk right"
def chunk_test():
- the_list = list(range(1, 57))
- results = divide_into_chunks(the_list, 7)
- print("results are:", results)
+ import random
+ random.seed(7)
+
+ number_exact = 0
+ total_amount_off = 0
+ for test in range(1, 1001):
+ print("\n\ntest:", test)
+ number_chunks = random.randint(1, 20)
+ number_elements = random.randint(0, 100)
+ the_list = list(range(1, number_elements))
+ result = divide_into_chunks(the_list, number_chunks)
+
+ print("Dividing list of length {} into approximately {} chunks - got {} chunks".format(
+ len(the_list), number_chunks, len(result)))
+ print("result:", result)
+
+ confirm_chunk(the_list, result)
+
+ amount_off = abs(number_chunks - len(result))
+ if amount_off == 0:
+ number_exact += 1
+ else:
+ total_amount_off += amount_off
+
+
+ print("\n{} exact out of {} [Total amount off: {}]".format(number_exact,
+ test,
+ total_amount_off))
+
+
+def chunk_test2():
+ import random
+ random.seed(7)
+
+ number_exact = 0
+ total_amount_off = 0
+
+ for test in range(1, 1001):
+ print("\n\ntest:", test)
+ number_chunks = random.randint(1, 20)
+ number_elements = random.randint(0, 100)
+ the_list = list(range(1, number_elements))
+ result = divide_into_chunks(the_list, number_chunks)
+ print("Dividing list of length {} into approximately {} chunks - got {} chunks".format(
+ len(the_list), number_chunks, len(result)))
+ print("result:", result)
+
+ amount_off = abs(number_chunks - len(result))
+ if amount_off == 0:
+ number_exact += 1
+ else:
+ total_amount_off += amount_off
+
+
+ print("\n{} exact out of {} [Total amount off: {}]".format(number_exact,
+ test,
+ total_amount_off))
+
+def old_chunk_test():
+
+ import random
+ random.seed(7)
+ for test in range(0, 10):
+ print("\n\ntest:", test)
+ num_elements = random.randint(0, 100)
+ the_list = list(range(1, num_elements))
+ num_chunks = random.randint(1, 20)
+ results = divide_into_chunks(the_list, num_chunks)
+ print("locals are:", locals())
+ print("results are:", results)
+ assert len(results) == num_chunks, "Didn't get number of chunks we expected"
+
def human_association(snp,
n,
keep,