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Divide large data files into smaller files


 
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Top Forums Shell Programming and Scripting Divide large data files into smaller files
# 1  
Old 07-16-2010
Divide large data files into smaller files

Hello everyone!

I have 2 types of files in the following format:

Code:
1) *.fa

>1234
...some text...
>2345
...some text...
>3456
...some text...
.
.
.
.

2) *.info

>1234
...some numbers...
>2345
...some numbers...
>3456
...some numbers...
.
.
.
.

I need to split these huge files (~300-400Mb), into smaller files (around 30-40Mb each). Also, I don't want to divide the data (i.e. every record starting with '>' should have its corresponding information in one smaller file).

Can someone please suggest a way to do this using unix commands?

Thanks!!!
# 2  
Old 07-17-2010
Could you please elaborate more on the criteria you want to use to split the file ?
# 3  
Old 07-17-2010
tell us your expect output

At first, you can use paste to make each record in one line.

Code:
$ paste - - < file.info
>1234   ...some numbers...
>2345   ...some numbers...
>3456   ...some numbers...

$ paste - - < file.fa
>1234   ...some text...
>2345   ...some text...
>3456   ...some text...


Last edited by rdcwayx; 07-17-2010 at 03:08 AM..
# 4  
Old 07-17-2010
use csplit
# 5  
Old 07-19-2010
Hello Everyone...
Thanks for your responses!!!

I need to divide my huge data file into smaller files (of say 10 MB or so). I have to feed this file ( as smaller sub-files) into another program.

The line numbers in each file vary. The program cannot take a huge file together, and needs chunks of data!!

I hope I am a little more clear now??

Thanks!
# 6  
Old 07-19-2010
You still don't tell us clearly what you ask for.

Give some real datas, and the expect output.
# 7  
Old 07-20-2010
Quote:
Originally Posted by ad23
...
I need to split these huge files (~300-400Mb), into smaller files (around 30-40Mb each). Also, I don't want to divide the data (i.e. every record starting with '>' should have its corresponding information in one smaller file).
If I correctly understand your requirement and assuming the above format of the big files,
Code:
awk '/^>[0-9]+$/ && c >=int(n/s) { k++; c=1; close(f) }
     { print > (f=FILENAME"_"k+1); c++ }' s=10 n="$(wc -l < bigfile)" bigfile

For different smaller files' sizes adjust the value of the variable s.

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