def convert_orthologs_for_upload(infile, outfile):
'''
The Ortholog Benchmarking website expects orthologs in a file
where each line has an ortholog, represented as a pair of sequence
ids separated by a tab.
http://linneus54.inf.ethz.ch:8080/cgi-bin/gateway.pl
'''
with open(outfile, 'w') as fh:
for params, orthologs in orthutil.orthDatasFromFileGen(infile):
for qdb, sdb, distance in orthologs:
fh.write('{qdb}\t{sdb}\n'.format(**locals()))
def load_orth_datas(ds):
'''
load orthDatas serially. takes a long time. use dones to resume job if it dies.
'''
release = roundup.dataset.getDatasetId(ds)
print 'getting ids'
genomeToId = roundup_db.getGenomeToId(release)
divToId = roundup_db.getDivergenceToId(release)
evalueToId = roundup_db.getEvalueToId(release)
geneToId = roundup_db.getSequenceToId(release)
print 'loading orthDatas'
for path in roundup.dataset.getOrthologsFiles(ds):
if get_dones(ds).done(path):
print 'already loaded:', path
else:
print 'loading', path
orthDatasGen = orthutil.orthDatasFromFileGen(path)
roundup_db.loadReleaseResults(release, genomeToId, divToId, evalueToId, geneToId, orthDatasGen)
get_dones(ds).mark(path)
print 'done loading all orthDatas'
