def search(args):
"""
Return features within a chromosomal region in JBrowse JSON format
"""
q = args['q']
chrom = None if 'chr' not in args \
else args['chr']
start = None if 'start' not in args \
else args['start']
end = None if 'end' not in args \
else args['end']
if start >= end:
tools.fail('End coordinate must be greater than start')
strand = None if 'strand' not in args \
else args['strand']
featuretype = 'mRNA' if 'featuretype' not in args \
else args['featuretype']
completely_within = False if 'completely_within' not in args \
else args['completely_within']
level = 1 if 'level' not in args \
else args['level']
imfeatureclass = tools.to_camel_case(featuretype)
if q == 'features':
data = utils.get_features(refseq=chrom, start=start, \
end=end, strand=strand, featuretype=imfeatureclass,
completely_within=completely_within, level=level)
if not data:
return tools.fail('Failed to retrieve feature data in JSON')
elif q == 'globalStats':
data = utils.get_global_stats(featuretype=imfeatureclass)
elif q == 'regionStats':
data = utils.get_region_stats(refseq=chrom, start=start, \
end=end, featuretype=imfeatureclass)
elif q == 'regionFeatureDensities':
data = utils.get_region_feature_densities(refseq=chrom, start=start, \
end=end, featuretype=imfeatureclass)
return 'application/json', json.dumps(data)
def search(args):
"""
Return features within a chromosomal region in JBrowse JSON format
"""
q = args['q']
chrom = args['chr']
start = args['start']
end = args['end']
if start >= end:
tools.fail('End coordinate must be greater than start')
strand = None if 'strand' not in args \
else args['strand']
featuretype = 'mRNA' if 'featuretype' not in args \
else args['featuretype']
level = 1 if 'level' not in args \
else args['level']
completely_within = False if 'completely_within' not in args \
else args['completely_within']
interbase = True if 'interbase' not in args \
else args['interbase']
if q == 'features':
data = utils.parse_gff(gff_file, chrom=chrom, start=start, \
end=end, strand=strand, featuretype=featuretype, level=level, \
completely_within=completely_within, interbase=interbase)
if not data:
return tools.fail('Failed to parse gff')
elif q == 'globalStats':
data = { 'scoreMin': -1, 'scoreMax': 1 }
elif q == 'regionStats':
raise Exception('Not implemented yet')
elif q == 'regionFeatureDensities':
raise Exception('Not implemented yet')
return 'application/json', json.dumps(data)
