def search(args):
"""
args contains a dict with one or key:values
locus is AGI identifier and is mandatory
"""
search_locus = args['locus']
"""
Parse the local Araport11 gff3 file to find the search locus
"""
locus_record = None
with gzip.open(ARAPORT11_GFF, 'r') as f:
for header, data in tools.read_block(f, '###'):
gene_fields = data[0].split('\t')
locus = tools.extract_agi_identifier(gene_fields[8])
if search_locus == locus:
locus_record = data
break
"""
Iterate through the results
Foreach record from the remote service, build the response json
Print this json to stdout followed by a record separator "---"
ADAMA takes care of serializing these results
"""
response = tools.parse_gff_block(locus_record)
print json.dumps(response, indent=2)
print '---'
def list(args):
"""
List all of the available loci from the Araport11 protein-coding gene set
"""
with gzip.open(ARAPORT11_GFF, 'r') as f:
for header, data in tools.read_block(f, '###'):
gene_fields = data[0].split('\t')
locus = tools.extract_agi_identifier(gene_fields[8])
record = {
'locus': locus,
'class': 'locus_property',
'source_text_description': 'Araport11 locus'
}
print json.dumps(record, indent=2)
print '---'
