[Tutor] large file
cristetoespiritante at gmail.com
Mon Jun 14 13:08:13 CEST 2010
Alan Gauld wrote:
> "Hs Hs" <ilhs_hs at 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
> 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...
> Alan Gauld
> Author of the Learn to Program web site
> Tutor maillist - Tutor at python.org
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Thanks for this thread. This is very helful. I'm learning a lot from you
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