From 5bc21b394229efd944e202c0c769a5423ba64ef1 Mon Sep 17 00:00:00 2001 From: Marcus Stoiber Date: Mon, 25 Oct 2021 16:20:36 -0700 Subject: [PATCH] Fix bugs in current master due to post_out switch --- megalodon/backends.py | 6 +++--- megalodon_extras/calibrate_generate_mod_stats_from_msf.py | 1 + megalodon_extras/calibrate_generate_variant_stats.py | 1 + 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/megalodon/backends.py b/megalodon/backends.py index 194dcca..e23f9ec 100755 --- a/megalodon/backends.py +++ b/megalodon/backends.py @@ -208,9 +208,9 @@ def parse_backend_params(args, num_fast5_startup_reads=5): args.guppy_server_port = "auto" # only start server with post out if flip-flop mods or variants are # requested - post_out = ( - mh.PR_MOD_NAME in args.outputs and args.remora_model is None - ) or mh.PR_VAR_NAME in args.outputs + post_out = hasattr(args, "outputs") and ( + mh.PR_MOD_NAME in args.outputs or mh.PR_VAR_NAME in args.outputs + ) pyguppy_params = PYGUPPY_PARAMS( available=True, config=args.guppy_config, diff --git a/megalodon_extras/calibrate_generate_mod_stats_from_msf.py b/megalodon_extras/calibrate_generate_mod_stats_from_msf.py index d184bb1..bddc322 100644 --- a/megalodon_extras/calibrate_generate_mod_stats_from_msf.py +++ b/megalodon_extras/calibrate_generate_mod_stats_from_msf.py @@ -377,6 +377,7 @@ def _main(args): + "guppy logs." ) args = add_trim_guppy_none(args) + args.outputs = [mh.PR_MOD_NAME] # make edge_buffer >= context_bases to simplify processing if args.edge_buffer < args.mod_context_bases: LOGGER.warning( diff --git a/megalodon_extras/calibrate_generate_variant_stats.py b/megalodon_extras/calibrate_generate_variant_stats.py index 0a9e7bc..701a441 100755 --- a/megalodon_extras/calibrate_generate_variant_stats.py +++ b/megalodon_extras/calibrate_generate_variant_stats.py @@ -645,6 +645,7 @@ def _main(args): # this script. args.do_not_use_guppy_server = False args.output_directory = args.guppy_logs_output_directory + args.outputs = [mh.PR_VAR_NAME] LOGGER.info("Loading model.") backend_params = backends.parse_backend_params(args)