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Code is working slow - performance issue in python

I have file which has 4 columns with, separated values. I need only first column only so I have read file then split that line with, separated and store it in one list variable called first_file_list.
I have another file which has 6 columns with, separated values. My requirement is read first column of first row of file and check that string is exist in list called first_file_list. If that is exist then copy that line to new file.
My first file has approx. 6 million records and second file has approx. 4.5 million records. Just to check the performance of my code instead of 4.5 million I have put only 100k records in second file and to process the 100k record code takes approx. 2.5 hours.
Following is my logic for this:
first_file_list = []
with open("c:\first_file.csv") as first_f:
next(first_f) # Ignoring first row as it is header and I don't need that
temp = first_f.readlines()
for x in temp:
first_file_list.append(x.split(',')[0])
first_f.close()
with open("c:\second_file.csv") as second_f:
next(second_f)
second_file_co = second_f.readlines()
second_f.close()
out_file = open("c:\output_file.csv", "a")
for x in second_file_co:
if x.split(',')[0] in first_file_list:
out_file.write(x)
out_file.close()
Can you please help me to get to know that what I am doing wrong here so that my code take this much time to compare 100k records? or can you suggest better way to do this in Python.

Use a set for fast membership checking.
Also, there's no need to copy the contents of the entire file to memory. You can just iterate over the remaining contents of the file.
first_entries = set()
with open("c:\first_file.csv") as first_f:
next(first_f)
for line in first_f:
first_entries.add(line.split(',')[0])
with open("c:\second_file.csv") as second_f:
with open("c:\output_file.csv", "a") as out_file:
next(second_f)
for line in second_f:
if line.split(',')[0] in first_entries:
out_file.write(line)
Additionally, I noticed you called .close() on file objects that were opened with the with statement. Using with (context managers) means all the clean up is done after you exit its context. So it handles the .close() for you.

work with sets - see below
first_file_values = set()
second_file_values = set()
with open("c:\first_file.csv") as first_f:
next(first_f)
temp = first_f.readlines()
for x in temp:
first_file_values.add(x.split(',')[0])
with open("c:\second_file.csv") as second_f:
next(second_f)
second_file_co = second_f.readlines()
for x in second_file_co:
second_file_values.add(x.split(',')[0])
with open("c:\output_file.csv", "a") as out_file:
for x in second_file_values:
if x in first_file_values:
out_file.write(x)

Change from array of specified size to dynamic array?

I have a program that's looking for certain values in a log file and listing them out. Essentially, one line of a 50000 line file would look like this:
Step Elapsed Temp Press Volume TotEng KinEng PotEng E_mol E_pair Pxx Pyy Pzz Pxz Pxy Pyz
0 0 298 -93.542117 448382.78 -67392.894 17986.81 -85379.704 12349.955 -97729.659 -313.09273 44.936408 -12.47003 100.97953 -215.4029 254.07517
10 10 301.05619 -14.956923 448382.78 -66191.142 18171.277 -84362.419 12474.283 -96836.702 -56.794471 103.79453 -91.870824 300.09707 -27.638439 196.2738
The bit of code that's doing the searching and appending looks like this:
line=fp.readline()
while line:
line=fp.readline()
words = line.split()
if (words[0]=="Step"):
break
numcol = len(words)
header = words
data = numpy.zeros((numcol,100000))
ln = 0
while line:
line=fp.readline()
words=line.split()
if(words[0]=="Loop"):
break
for i in range(numcol):
data[i][ln]=(float(words[i]))
ln_original = ln
ln = ln +1
Currently, I'm specifying the number of columns in my array. I can't seem to figure out how to get appending to work. Any ideas as to what I could change so that the array can be dynamic for log files of various lengths instead of specifying something like 1,000,000 lines in the array to begin with?

make a list of lists and append items to those lists. when you get to the end of the file cast the list of lists to a np.ndarray.
change
data = numpy.zeros((numcol,100000))
to
data = [[] for i in range(numcol)]
and change
data[i][ln]=(float(words[i]))
to
data[i].append(float(words[i]))
at the end of the code add
data = np.array(data)

Arranging distinct number of floats in an 2d array

First of all I am quite a newbie on python, so please forgive me if I don't see the wood for the trees. My question is on reading a huge file of float numbers and storing them in an array for fast mathematical postprocessing.
Lets assume the file looks similar to this:
!!
-3.2297390 0.4474691 3.5690145 3.5976372 6.9002712 7.7787466 14.2159269 14.3291490
16.7660723 17.1258704 18.9469059 19.1716808 20.0700721 21.4088414
-3.2045361 0.4123081 3.5625981 3.5936954 6.8901539 7.7543415 14.2764611 14.3623976
16.7955934 17.1560337 18.9527369 19.1251184 20.0700709 21.3515145
-3.2317597 0.4494166 3.5799182 3.6005429 6.8838705 7.7661897 14.2576455 14.3295731
16.7550357 17.0986678 19.0187779 19.1687722 20.0288587 21.3818250
-3.1921346 0.3949598 3.5636878 3.5892085 6.8833690 7.7404542 14.3061281 14.3855389
16.8063645 17.1697110 18.9549920 19.1134580 20.0613223 21.3196066
here there are 4 (nb) blocks of 14 (nk) float numbers each. I want them to be arranged in an array elements[nb][nk] so that I can access easily looping over certain floats of the blocks.
Here is what I thought it should look like, but it doesn't work at all:
nb=4
nk=14
with open("datafile") as file:
elements = []
n = 0
while '!!' not in file:
while n <= (nb-1):
elements.append([])
current = map(float,file.read().split()) # here I would need something to assure only 14 (nk) floats are read in
elements[n].append(current)
n += 1
print(elements[0][1])
It would be great if had some ideas and suggestions. Thanks!
EDIT:
here an datafile where the numbers follow after each other with no clear seperator after a block nb. Here it is nb=2 and nk=160. How to split the read in floats after each 160th number?
!!
-7.2578105433 -7.2578105433 -6.7774609392 -6.7774609392 -6.3343986693 -6.3343986693 -5.8537216826 -5.8537216826
-5.6031029888 -5.6031029888 -2.9103190893 -2.9103190893 -1.7962279174 -1.7962279174 -0.8136720023 -0.8136720023
-0.1418500769 -0.1418500769 2.9923464558 2.9923464558 3.5797768050 3.5797768050 3.8793240270 3.8793240270
4.0774192689 4.0774192689 4.2378755781 4.2378755781 4.2707165126 4.2707165126 4.3290523910 4.3290523910
4.4487102661 4.4487102661 4.5341883539 4.5341883539 4.7946098470 4.7946098470 4.9518205998 4.9518205998
4.9592549825 4.9592549825 5.1648268937 5.1648268937 5.2372127454 5.2372127454 5.9377062691 5.9377062691
6.2971992823 6.2971992823 6.6324702419 6.6324702419 6.7948808733 6.7948808733 7.0835270703 7.0835270703
7.6252686579 7.6252686579 7.7886279100 7.7886279100 7.8514022664 7.8514022664 7.9188180854 7.9188180854
7.9661386138 7.9661386138 8.2830991934 8.2830991934 8.4581462733 8.4581462733 8.5537201519 8.5537201519
10.2738010533 10.2738010533 11.4495306517 11.4495306517 11.4819579346 11.4819579346 11.5788238984 11.5788238984
11.9411469341 11.9411469341 12.5006172267 12.5006172267 12.5055546075 12.5055546075 12.6659410418 12.6659410418
12.8741094000 12.8741094000 12.9560279595 12.9560279595 12.9780521671 12.9780521671 13.2195973082 13.2195973082
13.2339969658 13.2339969658 13.3594047155 13.3594047155 13.4530024795 13.4530024795 13.4556342387 13.4556342387
13.5784994631 13.5784994631 14.6887369915 14.6887369915 14.9019726334 14.9019726334 15.1279383300 15.1279383300
15.1953349879 15.1953349879 15.3209538297 15.3209538297 15.4042612992 15.4042612992 15.4528348692 15.4528348692
15.4542742538 15.4542742538 15.5291462589 15.5291462589 15.5415591416 15.5415591416 16.0741610117 16.0741610117
16.1117432607 16.1117432607 16.3566675522 16.3566675522 17.7569123657 17.7569123657 18.4416346230 18.4416346230
18.9525843134 18.9525843134 19.0591624486 19.0591624486 19.1069867477 19.1069867477 19.1853525353 19.1853525353
19.4020021909 19.4020021909 19.4718240723 19.4718240723 19.6384650104 19.6384650104 19.6919638323 19.6919638323
19.7044699790 19.7044699790 19.8851141335 19.8851141335 20.6132283388 20.6132283388 21.4074471478 21.4074471478
-7.2568288331 -7.2568280628 -6.7765483088 -6.7765429702 -6.3336003082 -6.3334841531 -5.8529872639 -5.8528369047
-5.6024822566 -5.6024743589 -2.9101060346 -2.9100930470 -1.7964872791 -1.7959333994 -0.8153333579 -0.8144924713
-0.1440078470 -0.1421444935 2.9869228390 2.9935342026 3.5661875018 3.5733148387 3.8777649741 3.8828300867
4.0569348321 4.0745074351 4.2152251981 4.2276050415 4.2620483420 4.2649182323 4.3401804124 4.3402590222
4.4446178512 4.4509411587 4.5139270348 4.5526439516 4.7788285567 4.7810706248 4.9282976775 4.9397807768
4.9737752749 4.9900180286 5.1456209436 5.1507667583 5.2528363215 5.2835144984 5.9252188817 5.9670441193
6.2699491148 6.3270140700 6.5912060019 6.6576016532 6.7976670773 6.7982056614 7.0789050974 7.1023337244
7.6182108739 7.6309688587 7.7678148773 7.7874194913 7.8544608005 7.8594983757 7.9019395451 7.9100447766
7.9872550937 7.9902791771 8.2617740182 8.3147140843 8.4533756827 8.4672364683 8.5556163680 8.5558640539
10.2756173692 10.2760227976 11.4344757209 11.4355375519 11.4737803653 11.4760186102 11.5914333288 11.5953932241
11.9369518613 11.9380900159 12.4973099542 12.5002401499 12.5030167542 12.5031963862 12.6629548222 12.6634150863
12.8719844312 12.8728126622 12.9541436501 12.9568445777 12.9762780998 12.9764840239 13.2074024551 13.2108294169
13.2279146175 13.2308902307 13.3780648962 13.3839050348 13.4634576072 13.4650575047 13.4701414823 13.4718238883
13.5901622459 13.5971076111 14.6735704782 14.6840793519 14.8963924604 14.8968395615 15.1163287408 15.1219631271
15.1791724308 15.1817299995 15.2628531102 15.3027136606 15.3755066968 15.3802521520 15.3969012144 15.4139294088
15.5131322524 15.5315039463 15.5465532500 15.5629105034 15.5927166831 15.5966393750 16.0841067052 16.0883417123
16.1224821534 16.1226510159 16.3646268213 16.3665839987 17.7654543366 17.7657216551 18.4305335335 18.4342292730
18.9110142692 18.9215889808 18.9821593138 18.9838270736 19.1633959849 19.1637558341 19.2040877093 19.2056062802
19.3760597529 19.3846323861 19.4323552578 19.4329488797 19.6494790293 19.6813374885 19.6943820824 19.7202356536
19.7381237231 19.7414645409 19.9056461663 19.9197428869 20.6239183178 20.6285756411 21.4127637743 21.4128909767

This should work:
elements = []
with open("datafile") as file:
next(file)
for line in file:
elements.append([float(x) for x in line.split()])
next(line) reads the first line. Then for line in file: iterates over all other lines. The list comprehension [float(x) for x in line.split()] goes through all entries in the line split by whitespace. Finally, elements.append() appends this list to elements, which becomes a list of lists that you can call an 2D array.
Access the first entry in the first line:
>>> elements[0][0]
-3.229739
or the last entry in the last line:
>>> elements[3][13]
21.319606
alternatively:
>>> elements[-1][-1]
21.319606
Update
This reads the file into a list of lists without taking line breaks as special:
nb = 2
nk = 160
with open("datafile") as fobj:
all_values = iter(x for x in fobj.read().split())
next(all_values)
elements = []
for x in range(nb):
elements.append([float(next(all_values)) for counter in range(nk)])
If you like nested list comprehensions:
with open("datafile") as fobj:
all_values = iter(x for x in fobj.read().split())
next(all_values)
elements = [[float(next(all_values)) for counter in range(nk)] for x in range(nb)]

Extraction and processing the data from txt file

I am beginner in python (also in programming)I have a larg file containing repeating 3 lines with numbers 1 empty line and again...
if I print the file it looks like:
1.93202838
1.81608154
1.50676177
2.35787777
1.51866227
1.19643624
...
I want to take each three numbers - so that it is one vector, make some math operations with them and write them back to a new file and move to another three lines - to another vector.so here is my code (doesnt work):
import math
inF = open("data.txt", "r+")
outF = open("blabla.txt", "w")
a = []
fin = []
b = []
for line in inF:
a.append(line)
if line.startswith(" \n"):
fin.append(b)
h1 = float(fin[0])
k2 = float(fin[1])
l3 = float(fin[2])
h = h1/(math.sqrt(h1*h1+k1*k1+l1*l1)+1)
k = k1/(math.sqrt(h1*h1+k1*k1+l1*l1)+1)
l = l1/(math.sqrt(h1*h1+k1*k1+l1*l1)+1)
vector = [str(h), str(k), str(l)]
outF.write('\n'.join(vector)
b = a
a = []
inF.close()
outF.close()
print "done!"
I want to get "vector" from each 3 lines in my file and put it into blabla.txt output file. Thanks a lot!

My 'code comment' answer:
take care to close all parenthesis, in order to match the opened ones! (this is very likely to raise SyntaxError ;-) )
fin is created as an empty list, and is never filled. Trying to call any value by fin[n] is therefore very likely to break with an IndexError;
k2 and l3 are created but never used;
k1 and l1 are not created but used, this is very likely to break with a NameError;
b is created as a copy of a, so is a list. But you do a fin.append(b): what do you expect in this case by appending (not extending) a list?
Hope this helps!

This is only in the answers section for length and formatting.
Input and output.
Control flow
I know nothing of vectors, you might want to look into the Math module or NumPy.
Those links should hopefully give you all the information you need to at least get started with this problem, as yuvi said, the code won't be written for you but you can come back when you have something that isn't working as you expected or you don't fully understand.

Optimize python file comparison script

I have written a script which works, but I'm guessing isn't the most efficient. What I need to do is the following:
Compare two csv files that contain user information. It's essentially a member list where one file is a more updated version of the other.
The files contain data such as ID, name, status, etc, etc
Write to a third csv file ONLY the records in the new file that either don't exist in the older file, or contain updated information. For each record, there is a unique ID that allows me to determine if a record is new or previously existed.
Here is the code I have written so far:
import csv
fileAin = open('old.csv','rb')
fOld = csv.reader(fileAin)
fileBin = open('new.csv','rb')
fNew = csv.reader(fileBin)
fileCout = open('NewAndUpdated.csv','wb')
fNewUpdate = csv.writer(fileCout)
old = []
new = []
for row in fOld:
old.append(row)
for row in fNew:
new.append(row)
output = []
x = len(new)
i = 0
num = 0
while i < x:
if new[num] not in old:
fNewUpdate.writerow(new[num])
num += 1
i += 1
fileAin.close()
fileBin.close()
fileCout.close()
In terms of functionality, this script works. However I'm trying to run this on files that contain hundreds of thousands of records and it's taking hours to complete. I am guessing the problem lies with reading both files to lists and treating the entire row of data as a single string for comparison.
My question is, for what I am trying to do is this there a faster, more efficient, way to process the two files to create the third file containing only new and updated records? I don't really have a target time, just mostly wanting to understand if there are better ways in Python to process these files.
Thanks in advance for any help.
UPDATE to include sample row of data:
123456789,34,DOE,JOHN,1764756,1234 MAIN ST.,CITY,STATE,305,1,A

How about something like this? One of the biggest inefficiencies of your code is checking whether new[num] is in old every time because old is a list so you have to iterate through the entire list. Using a dictionary is much much faster.
import csv
fileAin = open('old.csv','rb')
fOld = csv.reader(fileAin)
fileBin = open('new.csv','rb')
fNew = csv.reader(fileBin)
fileCout = open('NewAndUpdated.csv','wb')
fNewUpdate = csv.writer(fileCout)
old = {row[0]:row[1:] for row in fOld}
new = {row[0]:row[1:] for row in fNew}
fileAin.close()
fileBin.close()
output = {}
for row_id in new:
if row_id not in old or not old[row_id] == new[row_id]:
output[row_id] = new[row_id]
for row_id in output:
fNewUpdate.writerow([row_id] + output[row_id])
fileCout.close()

difflib is quite efficient: http://docs.python.org/library/difflib.html

Sort the data by your unique field(s), and then use a comparison process analogous to the merge step of merge sort:
http://en.wikipedia.org/wiki/Merge_sort