Hi, Chris! It's working for me. Here's what I did:
mkdir chris cd chris wget http://genomewiki.ucsc.edu/images/7/72/BlatBot_pl.txt mv BlatBot_pl.txt BlatBot.pl chmod +x BlatBot.pl vi query.fa >NM_000454.4 gtttggggccagagtgggcgaggcgcggaggtctggcctataaagtagtc gcggagacggggtgctggtttgcgtcgtagtctcctgcagcgtctggggt ttccgttgcagtcctcggaaccaggacctcggcgtggcctagcgagttat ggcgacgaaggccgtgtgcgtgctgaagggcgacggcccagtgcagggca tcatcaatttcgagcagaaggaaagtaatggaccagtgaaggtgtgggga agcattaaaggactgactgaaggcctgcatggattccatgttcatgagtt tggagataatacagcaggctgtaccagtgcaggtcctcactttaatcctc tatccagaaaacacggtgggccaaaggatgaagagaggcatgttggagac ttgggcaatgtgactgctgacaaagatggtgtggccgatgtgtctattga agattctgtgatctcactctcaggagaccattgcatcattggccgcacac tggtggtccatgaaaaagcagatgacttgggcaaaggtggaaatgaagaa agtacaaagacaggaaacgctggaagtcgtttggcttgtggtgtaattgg gatcgcccaataaacattcccttggatgtagtctgaggccccttaactca tctgttatcctgctagctgtagaaatgtatcctgataaacattaaacact gtaatcttaaaagtgtaattgtgtgactttttcagagttgctttaaagta cctgtagtgagaaactgatttatgatcacttggaagatttgtatagtttt ataaaactcagttaaaatgtctgtttcaatgacctgtattttgccagact taaatcacagatgggtattaaacttgtcagaatttctttgtcattcaagc ctgtgaataaaaaccctgtatggcacttattatgaggctattaaaagaat ccaaattcaaactaaaaaaaaaaaaaaaaaa ./BlatBot.pl Human hg19 RNA score query.fa hyperlink BlatBot.out wget http://genomewiki.ucsc.edu/images/6/6a/ParseBlatOutput.zip unzip ParseBlatOutput.zip ./parseBlatOutput.pl hyperlink BlatBot.out BLAT Search Results QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN --------------------------------------------------------------------------------------------------- NM_000454.4 962 1 966 981 100.0% 21 + 33031935 33041244 9310 NM_000454.4 383 81 708 981 82.1% 16 + 51141408 51142029 622 NM_000454.4 364 166 718 981 82.5% 8 - 126963993 126964539 547 NM_000454.4 180 753 961 981 93.3% 4 + 164581777 164581987 211 NM_000454.4 171 338 622 981 85.3% 6 - 53061509 53061783 275 NM_000454.4 25 333 364 981 75.0% 2 - 18692116 18692143 28 NM_000454.4 24 799 830 981 84.7% 2 + 170692265 170692294 30 NM_000454.4 22 727 749 981 100.0% 2 + 120554999 120555022 24 NM_000454.4 22 727 748 981 100.0% 17 + 18425175 18425196 22 NM_000454.4 22 262 287 981 84.0% 1 + 223250001 223250025 25 NM_000454.4 21 953 975 981 95.7% 2 - 63658599 63658621 23 NM_000454.4 21 507 528 981 100.0% 1 - 76611479 76611501 23 NM_000454.4 21 749 769 981 100.0% 4 + 49092888 49092908 21 -Galt On 09/13/11 14:01, Galt Barber wrote: > 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 > > 9/13/2011 11:47 AM, Buxton Chris (NORTH BRISTOL NHS TRUST): >> 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 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
