UNIX for Dummies Questions & Answers

Hi,
I have a text file with a very long string of characters, like "ACGCTTGCAA...", and I want to make another file with 36 characters from this string file every 4 lines like:

character of position 1 to position 36 of the string file, position 2-37, position 3-38 ... position length((string)-35)-length(string).
And in the other lines of the file write always the same strings like below:

@read
AACCCAGTAAGTCACAGTGCANCAAACTTGTTTATT
+read
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@read
ACCCAGTAAGTCACAGTGCANCAAACTTGTTTATTC
+read
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@read
CCCAGTAAGTCACAGTGCANCAAACTTGTTTATTCA
+read
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

So my question is, how can I do it?

Looks like DNA bases...

Code:

getconf LINE_MAX

This shows the longest possible string command line utilties can read from a file without err. On a lot of systems this is 2048. If your DNA-base string is longer than 2048 characters then you need C or perl, or python.

less than 2048:

Code:

awk ' { str=$0}
END{
 for(i=1; length(str) - i > 35; i++)
 {
	printf("%s\n%s\n%s\n%s\n",
		"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~",
		"@read",
		substr(str, i, 36),		
		"+read"
		)
 } } ' dnastringfile

Thanks for the info.
And what would be the code if each line would have only 36 characters like:

agcgagcgtttgagctggctgaacgtttgcagtcgt
tggcttgagctggctgaacgtttgcagtccgacgac

I guess now the code would be a bit more complicated since for example with the read from position 2 to 37 I would have to fetch characters from line 1 and 2.


Best regards and thanks in advance,
João