a2be3b4aee520bfa47602e50b4825b43e9854690 max Thu Dec 11 17:06:43 2014 -0800 small formatting changes in last commit diff --git src/hg/hgBeacon/hgBeacon src/hg/hgBeacon/hgBeacon index ab3e4bc..6e9b759 100755 --- src/hg/hgBeacon/hgBeacon +++ src/hg/hgBeacon/hgBeacon @@ -7,43 +7,43 @@ import cgi, subprocess, sys, cgitb, os, datetime from os.path import join, isfile cgitb.enable() # deactivate this on the RR, but useful for debugging: prints a http header on errors # dir for bigBed files and insdcToUcsc.tab DATADIR = "/gbdb/hg19/beacon" 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. + A Genomics Alliance Beacon at UCSC. - Data provided by Leiden Open Variation (Ivo Fokkema), Biobase/HGMD. + In collaboration with the Leiden Open Variation Database and Biobase/HGMD. parameters: - genome: ignored, always hg19/GRCh37 - chrom: either a number or X/Y or UCSC format like "chr1" or INSDC accession like CM000663.1 - dataset: either lovd or hgmd. This parameter can also be called "track" (backwards compatible) - pos: 0-based position, like 10042537 - allele: A,C,T,G. Ignored for HGMD (HGMD gives out only positions, not the - alleles, they are on the website) + alleles, they are only on their website) If the allele was found, returns the string "Yes", otherwise "No". For HGMD, an overlap with a variant is enough to trigger a "Yes", we don't have the alleles. For LOVD, an overlap with a short deletion or duplication returns "Maybe". Examples: http://%(host)s/cgi-bin/hgBeacon/hgBeacon?dataset=lovd&chrom=chr1&pos=808921&allele=A - returns "Yes" http://%(host)s/cgi-bin/hgBeacon/hgBeacon?dataset=hgmd?chrom=1&pos=2160493&allele=T - returns "Maybe", because the allele is in a small deletion Number of variants: - LOVD: 180k, version from Nov 2014