Good Afternoon Nicholas: It appears the error is from your use of the "next" variables. The "next" variables are used to back out with the "cancel" button.
You can eliminate the "next" variables, and instead use them without the "next" variables. This wget returns nothing for OP=any and all the alignments for OP=any: export OP=any wget -O t.html --timestamping \ "http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doIntersectPage=create&hgta_intersectGroup=genes&; hgta_intersectTrack=knownGene&hgta_intersectTable=knownGene&hgta_intersectOp=${OP}& boolshad.hgta_invertTable=0&boolshad.hgta_invertTable2=0&hgta_doIntersectSubmit=submit& clade=mammal&org=Human&db=hg19&hgta_group=compGeno&hgta_track=cons46way&hgta_table=multiz46way& hgta_regionType=range&position=chr11%3A50129327-50149612&hgta_outputType=maf&boolshad.sendToGalaxy=0& boolshad.sendToGreat=0&hgta_outFileName=&hgta_compressType=none&hgta_doTopSubmit=get+output" --Hiram Nicholas Price wrote: > Hi > > I have the location of a pseudogene chr11:50129327-50149612 in Human and I > am using multiz46way to find orthologous regions in other species. If I use > the intersection option "All multiz46way records that have any overlap with > UCSC Genes" on your website I get no homology which is the correct > answer. However if I use the following URL in my perl script I get an > alignment which is the same as when I use "All multiz46way records that have > no overlap with UCSC Genes". In other words if I change > "hgta_nextIntersectOp=any" to "hgta_nextIntersectOp=none" in my URL I get > the same answer, which is not right. Is there something wrong with the URL? > > $url = > " > http://genome.ucsc.edu/cgi-bin/hgTables?&hgta_doIntersectPage=create&hgta_nextIntersectGroup=genes&hgta_nextIntersectTrack > " > ."=knownGene&hgta_nextIntersectTable=knownGene&hgta_nextIntersectOp=any&hgta_nextMoreThreshold=80&hgta_nextLessThreshold" > ."=80&boolshad.hgta_nextInvertTable=0&boolshad.hgta_nextInvertTable2=0&hgta_doIntersectSubmit=submit" > ."&clade=mammal&org=Human&db=hg19&hgta_group=compGeno&hgta_track=cons46way&hgta_table=multiz46way" > ."&hgta_regionType=range&position=chr11%3A50129327-50149612&hgta_outputType=maf&boolshad.sendToGalaxy=0" > ."&boolshad.sendToGreat=0&hgta_outFileName=&hgta_compressType=none&hgta_doTopSubmit=get+output"; > > Nicholas _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
