d92a6079e9b8a9aed65ecde011a76b7e202aee8e max Thu Nov 20 14:22:48 2014 -0800 making the beacon help message a little bit better, refs #14393 diff --git src/beacon/query src/beacon/query index 036d9f4..00d90a1 100755 --- src/beacon/query +++ src/beacon/query @@ -1,149 +1,151 @@ #!/usr/bin/env python # a beacon for LOVD, ClinVar, UniProt and HGMD, see ga4gh.org/#/beacon import cgi, subprocess, sys, cgitb, os, datetime, gdbm cgitb.enable() trackFnames = { "clinvar" : "clinvarMain.bb", "uniprot" : "spMut.bb", "hgmd" : "hgmd.bb", "lovd" : "lovd.bb" } MAXREQPERDAY=1000 def checkReqCount(): " check if IP address has exceeded max number of requests today " accCounts = gdbm.open("accCounts.gdbm", "c") ipAddr = os.environ["REMOTE_ADDR"] dateStr = datetime.date.today().isoformat() accKey = ipAddr+"|"+dateStr try: oldCount = int(accCounts[accKey]) except KeyError: oldCount = 0 newCount = oldCount+1 if newCount > MAXREQPERDAY: print("No more requests left today") sys.exit(0) accCounts[accKey]=str(newCount) accCounts.close() def getTrackFromScript(): " check which track name occurs in script name, to make the track captured by symlinks " 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. 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 LOVD, an overlap with a deletion or duplication returns "Maybe". Examples: - http://hgwdev-max.cse.ucsc.edu/cgi-bin/beacon/query?track=lovd&chrom=chr1&pos=808921&allele=T - http://hgwdev-max.cse.ucsc.edu/cgi-bin/beacon/query?track=clinvar&chrom=chr1&pos=10042537&allele=T - http://hgwdev-max.cse.ucsc.edu/cgi-bin/beacon/query?track=uniprot&chrom=CM000663.1&pos=977027&allele=T + 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://hgwdev-max.cse.ucsc.edu/cgi-bin/beacon/queryLovd?chrom=1&pos=2160493&allele=T + http://%(host)s.cse.ucsc.edu/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") insdcToUcsc[name] = chrom print "Content-Type: text/html\n" form = cgi.FieldStorage() track = form.getfirst("track") if track is None: track = getTrackFromScript() chrom = form.getfirst("chrom") pos = form.getfirst("pos") nucl = form.getfirst("allele") # check parameters if chrom==None: errAbort() if not pos.isdigit(): errAbort("pos is not an int") if chrom.isdigit() or chrom in "XY": chrom = "chr"+chrom # convert chrom from genbank acc to ucsc string like "chr1" if chrom not in insdcToUcsc.values(): chrom = insdcToUcsc.get(chrom, None) if chrom==None: errAbort( "ERROR: illegal chrom identifier %s" % chrom) if track not in trackFnames: errAbort("illegal track name") if nucl==None or len(nucl)!=1 or nucl[0].lower() not in "actg": errAbort("invalid allele, can only be ACTG") checkReqCount() # change parameters slightly nucl = nucl.upper() fname = trackFnames[track] pos = int(pos) # run tool args = ["./bigBedToBed", fname, "stdout", "-chrom=%s"%chrom, "-start=%d"%pos, "-end=%d"%(pos+1)] p = subprocess.Popen(args, stdout=subprocess.PIPE) # parse output isMaybe = False for line in p.stdout: fs = line.rstrip("\n").split("\t") if fs[-1]=="maybe": isMaybe=True if int(fs[2])-int(fs[1])!=1 and track != "uniprot": continue if fs[3][-1]==nucl or track in ["hgmd", "uniprot"]: print "Yes" sys.exit(0) if isMaybe: print "Maybe" sys.exit(0) # cannot check exit code, no overlap triggers error #if p.returncode != 0: #print("Unable to run command") #sys.exit(0) print "No"