First of all, does bork.embl-heidelberg.de offer any sort of batch download, or text based save that could be used?

I'm guessing your looking to do this in a (semi) automated manner, and starting from saving as text from your web browser wont help in the long run, since your scripting the fetch? I also might suggest that you may want to consider contacting the web site maintainers. They may not be thrilled about getting hammered by your script, and may be very open to helping find an easier way to provide this information to you instead.

That being said, I used wget to download the page and wrote this code which seems to capture what you want (this is a quick translation from a command line test, and in no way should be considered production ready or tested).

while (<>) {
  chomp;
  if(/CANDIDATE (\d+)/){
    $cand = $1;
    @acc = ()
  } # if candidate line
  elsif (m{http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi}
      && m{(\w+)</A>}) {
    push(@acc,$1);
  } # else if ncbi accession #
  elsif (m{R-score</A>\s*=\s*(\S+);}) {
    print "$cand\t", join(",",@acc), "\t$1\n";
  } # else if R-score, print this candidates info
} # while reading web page

[download]

In reply to Re: regex with variable input by spq
in thread regex with variable input by BioGeek

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