Generators for processing large result sets - python-3.x

Question

I am retrieving information from a sqlite DB that gives me back around 20 million rows that I need to process. This information is then transformed into a dict of lists which I need to use. I am trying to use generators wherever possible.
Can someone please take a look at this code and suggest optimization please? I am either getting a “Killed” message or it takes a really long time to run. The SQL result set part is working fine. I tested the generator code in the Python interpreter and it doesn’t have any problems. I am guessing the problem is with the dict generation.
EDIT/UPDATE FOR CLARITY:
I have 20 million rows in my result set from my sqlite DB. Each row is of the form:
(2786972, 486255.0, 4125992.0, 'AACAGA', '2005’)
I now need to create a dict that is keyed with the fourth element ‘AACAGA’ of the row. The value that the dict will hold is the third element, but it has to hold the values for all the occurences in the result set. So, in our case here, ‘AACAGA’ will hold a list containing multiple values from the sql result set. The problem here is to find tandem repeats in a genome sequence. A tandem repeat is a genome read (‘AACAGA’) that is repeated atleast three times in succession. For me to calculate this, I need all the values in the third index as a list keyed by the genome read, in our case ‘AACAGA’. Once I have the list, I can subtract successive values in the list to see if there are three consecutive matches to the length of the read. This is what I aim to accomplish with the dictionary and lists as values.
#!/usr/bin/python3.3
import sqlite3 as sql
sequence_dict = {}
tandem_repeat = {}
def dict_generator(large_dict):
dkeys = large_dict.keys()
for k in dkeys:
yield(k, large_dict[k])
def create_result_generator():
conn = sql.connect('sequences_mt_test.sqlite', timeout=20)
c = conn.cursor()
try:
conn.row_factory = sql.Row
sql_string = "select * from sequence_info where kmer_length > 2"
c.execute(sql_string)
except sql.Error as error:
print("Error retrieving information from the database : ", error.args[0])
result_set = c.fetchall()
if result_set:
conn.close()
return(row for row in result_set)
def find_longest_tandem_repeat():
sortList = []
for entry in create_result_generator():
sequence_dict.setdefault(entry[3], []).append(entry[2])
for key,value in dict_generator(sequence_dict):
sortList = sorted(value)
for i in range (0, (len(sortList)-1)):
if((sortList[i+1]-sortList[i]) == (sortList[i+2]-sortList[i+1])
== (sortList[i+3]-sortList[i+2]) == (len(key))):
tandem_repeat[key] = True
break
print(max(k for k, v in tandem_repeat.items() if v))
if __name__ == "__main__":
find_longest_tandem_repeat()

Answer 1

I got some help with this on codereview as #hivert suggested. Thanks. This is much better solved in SQL rather than just code. I was new to SQL and hence could not write complex queries. Someone helped me out with that.
SELECT *
FROM sequence_info AS middle
JOIN sequence_info AS preceding
ON preceding.sequence_info = middle.sequence_info
AND preceding.sequence_offset = middle.sequence_offset -
length(middle.sequence_info)
JOIN sequence_info AS following
ON following.sequence_info = middle.sequence_info
AND following.sequence_offset = middle.sequence_offset +
length(middle.sequence_info)
WHERE middle.kmer_length > 2
ORDER BY length(middle.sequence_info) DESC, middle.sequence_info,
middle.sequence_offset;
Hope this helps someone with around the same idea. Here is a link to the thread on codereview.stackexchange.com