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Hello Everyone,

I need to read a .csv file which has a size of 2.26 GB . And I wrote a
Python script , where I need to read this file. And my Computer has 2
GB RAM Please see the code as follows:

"""
This program has been developed to retrieve all the promoter sequences
for the specified
list of genes in the given cluster

So, this program will act as a substitute to the whole EZRetrieve
system

Input arguments:

1) Cluster.txt or DowRatClust161718bwithDummy.txt
2) TransProCrossReferenceAndSequences.csv -> This is the file that has
all the promoter sequences
3) -2000
4) 500
"""

import time
import csv
import sys
import linecache
import re
from sets import Set
import gc

print time.localtime()

fileInputHandler = open(sys.argv[1],"r")
line = fileInputHandler.readline()

refSeqIDsinTransPro = []
promoterSequencesinTransPro = []
reader2 = csv.reader(open(sys.argv[2],"rb"))
reader2_list = []
reader2_list.extend(reader2)

for data2 in reader2_list:
refSeqIDsinTransPro.append(data2[3])
for data2 in reader2_list:
promoterSequencesinTransPro.append(data2[4])

while line:
l = line.rstrip('\n')
for j in range(1,len(refSeqIDsinTransPro)):
found = re.search(l,refSeqIDsinTransPro[j])
if found:
"""promoterSequencesinTransPro[j] """
print l

line = fileInputHandler.readline()


fileInputHandler.close()


The error that I got is given as follows:
Traceback (most recent call last):
File "RefSeqsToPromoterSequences.py", line 31, in <module>
reader2_list.extend(reader2)
MemoryError

I understand that the issue is Memory error and it is caused because
of the line reader2_list.extend(reader2). Is there any other
alternative method in reading the .csv file line by line?

sincerely,
Suprabhath

On Tue, Nov 11, 2008 at 7:47 AM, <> wrote:
> refSeqIDsinTransPro = []
> promoterSequencesinTransPro = []
> reader2 = csv.reader(open(sys.argv[2],"rb"))
> reader2_list = []
> reader2_list.extend(reader2)

Without testing, this looks like you're reading the _ENTIRE_
input stream into memory! Try this:

def readCSV(file):

if type(file) == str:
fd = open(file, "rU")
else:
fd = file

sniffer = csv.Sniffer()
dialect = sniffer.sniff(fd.readline())
fd.seek(0)

reader = csv.reader(fd, dialect)
for line in reader:
yield line

for line in readCSV(open("foo.csv", "r")):
...

--JamesMills

--
--
-- "Problems are solved by method"

On Nov 11, 8:47*am, tejsu...@gmail.com wrote:

> import linecache

Why???

> reader2 = csv.reader(open(sys.argv[2],"rb"))
> reader2_list = []
> reader2_list.extend(reader2)
>
> for data2 in reader2_list:
> * *refSeqIDsinTransPro.append(data2[3])
> for data2 in reader2_list:
> * *promoterSequencesinTransPro.append(data2[4])


All you need to do is replace the above by:

reader2 = csv.reader(open(sys.argv[2],"rb"))

for data2 in reader2:
refSeqIDsinTransPro.append(data2[3])
promoterSequencesinTransPro.append(data2[4])

On Nov 10, 4:47*pm, tejsu...@gmail.com wrote:
> Hello Everyone,
>
> I need to read a .csv file which has a size of 2.26 GB . And I wrote a
> Python script , where I need to read this file. And my Computer has 2
> GB RAM Please see the code as follows:
>
> """
> This program has been developed to retrieve all the promoter sequences
> for the specified
> list of genes in the given cluster
>
> So, this program will act as a substitute to the whole EZRetrieve
> system
>
> Input arguments:
>
> 1) Cluster.txt or DowRatClust161718bwithDummy.txt
> 2) TransProCrossReferenceAndSequences.csv -> This is the file that has
> all the promoter sequences
> 3) -2000
> 4) 500
> """
>
> import time
> import csv
> import sys
> import linecache
> import re
> from sets import Set
> import gc
>
> print time.localtime()
>
> fileInputHandler = open(sys.argv[1],"r")
> line = fileInputHandler.readline()
>
> refSeqIDsinTransPro = []
> promoterSequencesinTransPro = []
> reader2 = csv.reader(open(sys.argv[2],"rb"))
> reader2_list = []
> reader2_list.extend(reader2)
>
> for data2 in reader2_list:
> * *refSeqIDsinTransPro.append(data2[3])
> for data2 in reader2_list:
> * *promoterSequencesinTransPro.append(data2[4])
>
> while line:
> * *l = line.rstrip('\n')
> * *for j in range(1,len(refSeqIDsinTransPro)):
> * * * found = re.search(l,refSeqIDsinTransPro[j])
> * * * if found:
> * * * * *"""promoterSequencesinTransPro[j] *"""
> * * * * *print l
>
> * *line = fileInputHandler.readline()
>
> fileInputHandler.close()
>
> The error that I got is given as follows:
> Traceback (most recent call last):
> * File "RefSeqsToPromoterSequences.py", line 31, in <module>
> * * reader2_list.extend(reader2)
> MemoryError
>
> I understand that the issue is Memory error and it is caused because
> of the *line reader2_list.extend(reader2). Is there any other
> alternative method in reading the .csv file *line by line?
>
> sincerely,
> Suprabhath

Thanks a Lot James Mills. It worked