diff --git a/VERSION b/VERSION index 7e541aec6..6b4d15773 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.2.2 \ No newline at end of file +2.2.3 \ No newline at end of file diff --git a/autometa/binning/recursive_dbscan.py b/autometa/binning/recursive_dbscan.py index 35efa2b4f..a5b75fb81 100644 --- a/autometa/binning/recursive_dbscan.py +++ b/autometa/binning/recursive_dbscan.py @@ -186,7 +186,11 @@ def recursive_dbscan( coverage_stddev_cutoff=coverage_stddev_cutoff, gc_content_stddev_cutoff=gc_content_stddev_cutoff, ) - median_completeness = filtered_df.completeness.median() + if filtered_df.empty: + median_completeness = float("-inf") + else: + median_completeness = filtered_df.completeness.median() + if median_completeness >= best_median: best_median = median_completeness best_df = df @@ -379,7 +383,11 @@ def recursive_hdbscan( coverage_stddev_cutoff=coverage_stddev_cutoff, gc_content_stddev_cutoff=gc_content_stddev_cutoff, ) - median_completeness = filtered_df.completeness.median() + if filtered_df.empty: + median_completeness = float("-inf") + else: + median_completeness = filtered_df.completeness.median() + if median_completeness >= best_median: best_median = median_completeness best_df = df diff --git a/autometa/binning/utilities.py b/autometa/binning/utilities.py index 389eabc5d..6b2d0737d 100644 --- a/autometa/binning/utilities.py +++ b/autometa/binning/utilities.py @@ -31,6 +31,8 @@ import pandas as pd +import numpy as np + from typing import Iterable, Tuple from autometa.taxonomy.database import TaxonomyDatabase @@ -183,7 +185,9 @@ def add_metrics( # redundant_marker_count = cluster_marker_counts.gt(1).sum(axis=1) # calculate completeness and purity and std. dev. metrics completeness = present_marker_count / reference_markers_count * 100 + completeness = completeness.where(~np.isnan(completeness),pd.NA) purity = single_copy_marker_count / present_marker_count * 100 + purity = purity.where(~np.isnan(purity), pd.NA) coverage_stddev = main_grouped_by_cluster.coverage.std() gc_content_stddev = main_grouped_by_cluster.gc_content.std() # merge metrics with given dataframe diff --git a/nextflow.config b/nextflow.config index 5c311c683..9d9e7bad5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,7 +12,7 @@ manifest { doi = "https://doi.org/10.1093/nar/gkz148" mainScript = "main.nf" nextflowVersion = ">=21.04.0" - version = "2.2.2" + version = "2.2.3" }