fastaRegexFinder

[bioinfo4321]

Hi, Perhaps it's not an issue but my lack of understanding of the syntax, but I am not able to perform fuzzy regex seatch with your script. The syntax I am using is
-r "(ATGC){e<=1}"

It is not reporting any hits, whereas both exact and fuzzy matches exist in my input. Exact match without {e<=1} works just fine. Thank you.

[dariober]

Hi- fastaRegexFinder uses the standard re package for parsing regular expressions and I don't think it supports fuzzy matches. However, I may have a look at replacing the re package with regex`. Can you post some examples of what you are trying to do? (It may be that regexes are not the best solution...)

[bioinfo4321]

I want find patterns such as "ATGCGCAGAGCA" in whole genome fasta, get results by chromosome, start end. Your script pretty much does the job, except I want to allow mismatches (insetion, deletion or substitution) in the regex. Thanks.