Hi ,
Here is my first usable Python code.
The code works.
Here is what I'm trying to do.
I have two huge text files. After some processing, One is 12M (file A) and the
other 1M (file B) .
The files have columns which are of interest to me.
I 'm trying to match entries of column [0] on file A and B
If it is true proceed to find entries (Rows in file A) in range provided by
columns [1] [2] and [3] [4] in file B.
Column [1] and [3] define the lower bounds of the range
Column [3] and [4] define the upper bounds of the range
I also have put a variation of value so that I can lookup +/- var.
#/bin/python
import sys, os, csv, re
x = 0 #Define Zero for now
var = 1000000 #Taking the variation
# This programme finds the SNPs from the range passed
# csv splits columns and this file is tab spaced
fis = csv.reader(open("divs.map", "rb"), delimiter='\t', quoting=csv.QUOTE_NONE)
for row in fis:
# csv splits columns and this file is "," spaced
gvalues = csv.reader(open("genvalues", "rb"), delimiter=',',
quoting=csv.QUOTE_NONE)
for gvalue in gvalues:
# To see Columns (chr) Match
if row[0] == gvalue[0]:
# If Column 3 (range) is Zero print row
if int(gvalue[3]) == x:
a = int(gvalue[1]) - var
b = int(gvalue[2]) + var + 1
if int(a <= int(row[3]) <= b):
print row
# If Column 3 (range) is not zero find matches and print row
else:
a = int(gvalue[1]) - var
b = int(gvalue[2]) + var + 1
if int(a <= int(row[3]) <= b):
print row
c = int(gvalue[3]) - var
d = int(gvalue[4]) + var + 1
if int(c <= int(row[3]) <= d):
print row
-----------------------------------------------------
Question1 : Is there a better way ?
Question2 : For now I'm using shells time call for calculating time required.
Does Python provide a more fine grained check.
Question 2: If I have convert this code into a function.
Should I ?
def parse():
...
...
...
...
parse ()
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