def getRawResults(params):
'''
params: a 4-tuple of roundup params like (qdb, sdb, div, evalue).
returns: a string containing all the orthologs for the params. in the form external query sequence id, external subject sequence id, and distance
or None if the results do not exist.
'''
qdb, sdb, div, evalue = params
pair = roundup_common.makePair(qdb, sdb)
# get orthologs from db
orthologs = roundup_db.getOrthologs(release=webconfig.CURRENT_RELEASE,
qdb=pair[0], sdb=pair[1],
divergence=div, evalue=evalue)
# get a map to external sequence ids
sequenceIds = set()
for ortholog in orthologs:
sequenceIds.add(ortholog[0])
sequenceIds.add(ortholog[1])
sequenceIds = list(sequenceIds)
sequenceIdToSequenceDataMap = roundup_db.getSequenceIdToSequenceDataMap(
release=webconfig.CURRENT_RELEASE, sequenceIds=sequenceIds)
# format orthologs for download by mapping to external sequence ids.
results = None
if orthologs:
results = ''.join(['{}\t{}\t{}\n'.format(sequenceIdToSequenceDataMap[qid][roundup_common.EXTERNAL_SEQUENCE_ID_KEY],
sequenceIdToSequenceDataMap[sid][roundup_common.EXTERNAL_SEQUENCE_ID_KEY],
dist) for qid, sid, dist in orthologs])
return results
def getOrthData(params):
qdb, sdb, div, evalue = params
pair = roundup_common.makePair(qdb, sdb)
# get orthologs from db
dbOrthologs = roundup_db.getOrthologs(release=webconfig.CURRENT_RELEASE,
qdb=pair[0], sdb=pair[1],
divergence=div, evalue=evalue)
# get a map to external sequence ids
sequenceIds = set()
for ortholog in dbOrthologs:
sequenceIds.add(ortholog[0])
sequenceIds.add(ortholog[1])
sequenceIds = list(sequenceIds)
sequenceIdToSequenceDataMap = roundup_db.getSequenceIdToSequenceDataMap(
release=webconfig.CURRENT_RELEASE, sequenceIds=sequenceIds)
#
orthologs = [(sequenceIdToSequenceDataMap[qid][roundup_common.EXTERNAL_SEQUENCE_ID_KEY],
sequenceIdToSequenceDataMap[sid][roundup_common.EXTERNAL_SEQUENCE_ID_KEY],
str(dist)) for qid, sid, dist in dbOrthologs]
return (params, orthologs)