I was testing psl. I have found and fixed an additional screen-scraping problem (one extra leading space is now in the pattern needed), so this should make hyperlink blat output parse ok.
-Galt On 09/14/11 14:14, Buxton Chris (NORTH BRISTOL NHS TRUST) wrote: > I'm afraid its still not working, I can get it to output to a text file but > it is parsing out just the "------------" row from the html file (I ''ve run > all my BLAT queries as hyperlink output format) > > Chris > > -----Original Message----- > From: Galt Barber [mailto:[email protected]] > Sent: 13 September 2011 22:02 > To: Buxton Chris (NORTH BRISTOL NHS TRUST) > Cc: [email protected] > Subject: Re: [Genome] Problem with parseBlatOutput script for batch BLAT > submission data > > > Hi, Chris! > > http://genomewiki.ucsc.edu/index.php/Blat_Scripts > > I fixed the second script. It was screen-scraping the > blat html output, but that had changed so that it couldn't > identify the tag correctly. > > -Galt > > >> Hi, >> >> There are two perl scripts listed on >> http://genomewiki.ucsc.edu/index.php/Blat_Scripts to enable batch submission >> of sequences for homology comparisons to BLAT. >> >> I can get the submission one to work fine, but cant figure out why the >> second script that parses the output from the first (parseBlatOutput) >> doesn't seem to work with either html or psl format outputs from the batch >> submission script? >> >> Any help would be much appreciated, >> >> Thanks >> >> Chris >> >> > > > ******************************************************************************************************************** > > This message may contain confidential information. If you are not the > intended recipient please inform the > sender that you have received the message in error before deleting it. > Please do not disclose, copy or distribute information in this e-mail or take > any action in reliance on its contents: > to do so is strictly prohibited and may be unlawful. > > Thank you for your co-operation. > > NHSmail is the secure email and directory service available for all NHS staff > in England and Scotland > NHSmail is approved for exchanging patient data and other sensitive > information with NHSmail and GSi recipients > NHSmail provides an email address for your career in the NHS and can be > accessed anywhere > For more information and to find out how you can switch, visit > www.connectingforhealth.nhs.uk/nhsmail > > ******************************************************************************************************************** _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
