fuzzy comparison - how to extract text between two strings allowing for errors

Question

I use the following command to extract text between two strings in analyzing DNA sequences:

grep -o -h -P '(?<=CACAC).*(?=TGTGT)' foo.fastq

This works well for exact matches to "CACAC" or "TGTGT"

However, sometimes sequencing errors will produce an error, and instead of "CACAC", that line might have "CAAAC" (or any other one base error, insertion or deletion - CAAAC is just one example of the possible errors)

I have tried fuzzy matching with agrep, tre-agrep and have been unable to install ugrep.

While agrep works well with a single string, it does not seem to support extracting the sequence between two strings, at least using the syntax I use for grep.

Any suggestions?

Thanks in advance! -Steff2j

Answer 1

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