[wplug] Text searching

[Weber, Larry A]

Can the string you are searching for span multiple lines?

> -----Original Message-----
> From:	Doug Green [SMTP:Green at np.awing.upmc.edu]
> Sent:	Monday, March 17, 2003 9:07 AM
> To:	wplug at wplug.org
> Subject:	[wplug] Text searching
> 
> Hi all-
> 
> I have some large text files that I need to search. They are genomic
> sequences, and consist of 4 letters in a block of 10, separated by a
> space. There are 6 such blocks on a line, and each line is numbered for
> the order of the first letter (maybe 20,000+ lines per file?).
> Essentially, the format looks like this (obviously, the content is
> different):
> 
> 1       atacaatagg atacaatagg atacaatagg atacaatagg atacaatagg atacaatagg
> 61     atacaatagg atacaatagg atacaatagg atacaatagg atacaatagg atacaatagg
> 
> I need to be able to search within this kind of text file for a string of
> letters that is maybe 30-40 letters long, ignoring the spaces and numbers.
> The whole point is that I need to locate the position of my search string
> within the original text. Is there some fancy way to grep the file,
> ignoring spaces and numbers? Or to somehow filter out the spaces and
> numbers, creating a new file (maybe some cat option piped into a new
> file??)?
> 
> Any help/suggestions are greatly appreciated! Thanks!
> 
> Doug
>