INNER CODE UNIT · Python
i
torognes/swarm · scripts/graph_plot.py:94
if i == cluster - 1:
# Deal with ";size=" in a rather clumsy way... but it works
print("Reading target cluster", file=sys.stdout)
amplicons = [
tuple(
item.replace(";size=", "_").rstrip(";").rsplit("_", 1))
for item in swarm.strip().split(" ")]
break
# Drop amplicons with a low abundance (remove connections too)
if drop:
print("Excluding amplicons below threshold", file=sys.stdout)
amplicons = [amplicon for amplicon in amplicons
if int(amplicon[1]) > drop]
# Convert amplicon names to amplicon indexes (igraph uses
# numerical ids, not names). Requires python 2.7+)
amplicon_index = {amplicon[0]: i for (i, amplicon) in enumerate(amplicons)}