From 3dba46e357ff7f32ae4b541433ab617a031f02e3 Mon Sep 17 00:00:00 2001 From: Nicholas Noll Date: Wed, 12 Aug 2020 09:22:01 -0700 Subject: fix: remove profiling code --- pangraph/build.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/pangraph/build.py b/pangraph/build.py index 14f96d3..4d1a77f 100644 --- a/pangraph/build.py +++ b/pangraph/build.py @@ -71,12 +71,10 @@ def main(args): mkdir(tmp) log("aligning") - with cProfile.Profile() as pr: - T.align(tmp, args.len, args.mu, args.beta, args.extensive, args.statistics) - # TODO: when debugging phase is done, remove tmp directory + T.align(tmp, args.len, args.mu, args.beta, args.extensive, args.statistics) + # TODO: when debugging phase is done, remove tmp directory - graphs = T.collect() - pr.dump_stats("perf.prof") + graphs = T.collect() for i, g in enumerate(graphs): log(f"graph {i}: nseqs: {len(g.seqs)} nblks: {len(g.blks)}") -- cgit v1.2.1 From 8eb9feb037ef53e5c498335f22437195da5d437c Mon Sep 17 00:00:00 2001 From: Nicholas Noll Date: Wed, 12 Aug 2020 09:33:12 -0700 Subject: fix: remove profile import --- pangraph/build.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pangraph/build.py b/pangraph/build.py index 4d1a77f..01595b7 100644 --- a/pangraph/build.py +++ b/pangraph/build.py @@ -3,7 +3,6 @@ build a pangenome alignment from an annotated guide tree """ import os, sys import builtins -import cProfile from .utils import mkdir, log from .tree import Tree -- cgit v1.2.1