bd685aee85204e3c58ae67a4556b876b7ac43a57 max Fri Nov 21 02:14:05 2014 -0800 more beacon bugfixes, refs #14393 diff --git src/beacon/query src/beacon/query index 00d90a1..71a6970 100755 --- src/beacon/query +++ src/beacon/query @@ -37,50 +37,51 @@ name = sys.argv[0].lower() for trackName in trackFnames: if trackName in name: return trackName def errAbort(errMsg=None): print "

"
     if errMsg is not None:
         print "error: "+errMsg
 
     host = os.environ.get("HTTP_HOST", "")
 
     print """
     A Genomics Alliance Beacon at UCSC. In collaboration with the Leiden Open Variation Database.
 
-    Data provided by Leiden Open Variation (Ivo Fokkema), NCBI ClinVar, UniProt.
+    Data provided by Leiden Open Variation (Ivo Fokkema), NCBI ClinVar, UniProt, Biobase/HGMD.
 
     parameters:
     - chrom: either a number or X/Y or UCSC format like "chr1" or INSDC accession like CM000663.1
     - track: clinvar, uniprot or lovd
     - pos: 0-based position, like 10042537
     - allele: A,C,T,G. Ignored for UniProt (UniProt stores only amino acid changes)
 
     If the allele was found in the track, returns the string "Yes", otherwise "No".
 
-    For UniProt, an overlap with a amino acid change is enough to trigger "Yes".
+    For UniProt and HGMD, an overlap with an amino acid change is enough to trigger "Yes".
+    Therefore, the alleles are ignored for UniProt and HGMD.
     For LOVD, an overlap with a deletion or duplication returns "Maybe". 
 
     Examples:
     http://%(host)s/cgi-bin/beacon/query?track=lovd&chrom=chr1&pos=808921&allele=T
     http://%(host)s/cgi-bin/beacon/query?track=clinvar&chrom=chr1&pos=10042537&allele=T
     http://%(host)s/cgi-bin/beacon/query?track=uniprot&chrom=CM000663.1&pos=977027&allele=T
 
     Alternative URLs are queryLovd, queryClinvar and queryUniprot, e.g.
-    http://%(host)s.cse.ucsc.edu/cgi-bin/beacon/queryLovd?chrom=1&pos=2160493&allele=T
+    http://%(host)s/cgi-bin/beacon/queryLovd?chrom=1&pos=2160493&allele=T
     - returns "Maybe"
 
     Number of variants:
     - LOVD: 180k
     - ClinVar: 30k
     - HGMD: 90k
     - UniProt: 47k
     """ % locals()
     print "

" sys.exit(0) # parse INSDC -> ucsc chrom name table insdcToUcsc = {} for line in open("insdcToUcsc.tab"): name, chrom = line.rstrip("\n").split("\t")