"Hs Hs" <ilhs...@yahoo.com> wrote
I have a very large file 15Gb.
Every two lines are part of one readgroup.
I want to add two variables to every line.
HWUSI-EAS1211_0001:1:1:977:20764#0 RG:Z:2301
HWUSI-EAS1211_0001:1:1:977:20764#0 RG:Z:2302
...
Since I cannot read the entire file, I wanted to cat the file
What makes you think you cannot read the entire file?
something like this:
cat myfile | python myscript.py > myfile.sam
How does that help over Python reading the file line by line?
I do not know how to execute my logic after I read the line,
althought I tried:
while True:
second = raw_input()
x = second.split('\t')
Why are you splitting theline? You only need to append
data to the end of the line...
Could someone help me here either what I want to do.
In pseudo code:
open input and ouput files
read the first 14 lines from input
oddLine = True
while True:
read line from input
if oddLine:
append odd data
else
append evenData
write line to output file
oddLine = not oddLine
You probably want a try/except in there to catch the end of file.
This is not very different from the menu example in the file
handling topic of my tutorial...
HTH
--
Alan Gauld
Author of the Learn to Program web site
http://www.alan-g.me.uk/
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