def make_graph(max_hetdimer_bind, outfile):
'''Selects all active primers and outputs a primer compatibility graph.'''
# Reset all the primer IDs (as ids are only used for set_finder)
Primer.update(_id = -1).execute()
primers = list(Primer.select().where(Primer.active == True)
.order_by(Primer.ratio.desc()).execute())
if len(primers) == 0:
swga.error("No active sets found. Run `swga filter` first.")
for i, p in enumerate(primers):
p._id = i + 1
update_in_chunks(primers, show_progress=False)
swga.message("Composing primer compatibility graph...")
edges = graph.test_pairs(primers, max_hetdimer_bind)
if len(edges) == 0:
swga.error("No compatible primers. Try relaxing your parameters.", exception=False)
with open(outfile, 'wb') as out:
graph.write_graph(primers, edges, out)
def test_update_in_chunks(self, initdb, tprimers, seqs):
'''Must push all the updates successfully..'''
for primer in tprimers:
primer.fg_freq = 100
database.update_in_chunks(tprimers)
primers = Primer.select().where(Primer.seq << seqs)
for primer in primers:
assert primer.fg_freq == 100