Seems like you'd get much faster results by simply bulk-downloading the fasta files one time, and then use something faFrags to grab a region.
Also, you could make a .2bit file and twoBitToFa options to select any subset region from the 2bit file. -Galt On Fri, 14 Nov 2008, Gupta, Ashutosh (NIH/NCI) [F] wrote: > Hi, > > I want to be able to download genome sequences (without repeat masking, > all upper case) for a given chrNum with start & end coordinates. > > > > Here is how it is done on the browser: chrX:151,073,054-151,383,976 with > (0,0) flanking sequences upstream & downstream. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=115827007&o=151073053&g=getDna&; > i=mixed&c=chrX&l=151073053&r=151383976&db=hg18&hgsid=115827007 > > > > Is there a way to stitch together a url so that this data can be > generated (as if one was to press the getDNA button) or by the following > link: > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=115827007&g=htcGetDna2&table=&i > =mixed&o=151073053&l=151073053&r=151383976&getDnaPos=chrX%3A151%2C073%2C > 054-151%2C383%2C976&db=hg18&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.paddi > ng3=0&hgSeq.casing=upper&boolshad.hgSeq.maskRepeats=1&hgSeq.repMasking=l > ower&boolshad.hgSeq.revComp=1&submit=get+DNA > > > > The FAQs page suggests not to use the hgsid variable, and I am not sure > how to query without that. > > > > My question is pretty much the same as answered on the following page: > > http://www.soe.ucsc.edu/pipermail/genome/2008-August/017039.html > > , the only thing different is that I am not using a web browser. > > So creating or setting a session would not be helpful. > > > My program accepts a url & reads the content of the given url in html or > txt format. No browser is involved. > > > > All the necessary information has to be given in a single (or multiple) > link(s) / string(s), based on parameters defined in the example above: >> hg18_dna range=chrX:151073054-151383976 5'pad=0 3'pad=0 strand=+ > repeatMasking=none > > > > Any help would be much appreciated. > > Thanks, > > Ashutosh. > > > > PS: Is there a way to get the whole desired sequence in one line? > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
