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