diff --git a/vamb/__main__.py b/vamb/__main__.py index d653cf7e..d9942629 100755 --- a/vamb/__main__.py +++ b/vamb/__main__.py @@ -771,9 +771,11 @@ def cluster_and_write_files( print( str(i + 1), None if cluster.radius is None else round(cluster.radius, 3), - None - if cluster.observed_pvr is None - else round(cluster.observed_pvr, 2), + ( + None + if cluster.observed_pvr is None + else round(cluster.observed_pvr, 2) + ), cluster.kind_str, sum(sequence_lens[i] for i in cluster.members), len(cluster.members), diff --git a/vamb/aamb_encode.py b/vamb/aamb_encode.py index 689688cd..19f4ce85 100644 --- a/vamb/aamb_encode.py +++ b/vamb/aamb_encode.py @@ -1,6 +1,5 @@ """Adversarial autoencoders (AAE) for metagenomics binning, this files contains the implementation of the AAE""" - import numpy as np from math import log, isfinite import time diff --git a/vamb/semisupervised_encode.py b/vamb/semisupervised_encode.py index 8af77f86..ac81e58a 100644 --- a/vamb/semisupervised_encode.py +++ b/vamb/semisupervised_encode.py @@ -1,6 +1,5 @@ """Semisupervised multimodal VAEs for metagenomics binning, this files contains the implementation of the VAEVAE for MMSEQ predictions""" - __cmd_doc__ = """Encode depths and TNF using a VAE to latent representation""" import numpy as _np diff --git a/vamb/taxvamb_encode.py b/vamb/taxvamb_encode.py index 4c14a778..0854dde8 100644 --- a/vamb/taxvamb_encode.py +++ b/vamb/taxvamb_encode.py @@ -1,6 +1,5 @@ """Hierarchical loss for the labels suggested in https://arxiv.org/abs/2210.10929""" - __cmd_doc__ = """Hierarchical loss for the labels""" diff --git a/workflow_avamb/src/rip_bins.py b/workflow_avamb/src/rip_bins.py index 9287cbd7..e4fa705b 100644 --- a/workflow_avamb/src/rip_bins.py +++ b/workflow_avamb/src/rip_bins.py @@ -183,9 +183,9 @@ def remove_meaningless_edges_from_pairs( contig_length, ) print("Cluster ripped because of a meaningless edge ", cluster_updated) - clusters_changed_but_not_intersecting_contigs[ - cluster_updated - ] = cluster_contigs[cluster_updated] + clusters_changed_but_not_intersecting_contigs[cluster_updated] = ( + cluster_contigs[cluster_updated] + ) components: list[set[str]] = list() for component in nx.connected_components(graph_clusters): @@ -295,9 +295,9 @@ def make_all_components_pair( contig_length, ) print("Cluster ripped because of a pairing component ", cluster_updated) - clusters_changed_but_not_intersecting_contigs[ - cluster_updated - ] = cluster_contigs[cluster_updated] + clusters_changed_but_not_intersecting_contigs[cluster_updated] = ( + cluster_contigs[cluster_updated] + ) component_len = max( [ len(nx.node_connected_component(graph_clusters, node_i))