Merge pull request #90 from MicrobialDarkMatter/bump-pymethylation-utils

updated pymethylation_utils

nanomotif/_version.py

@@ -1 +1 @@
-__version__ = "0.5.0"
+__version__ = "0.5.1"

nanomotif/main.py

@@ -441,7 +441,7 @@ def check_install(args, pl):
 # Binnary - contamination and inclusion
 from nanomotif.binnary import data_processing, detect_contamination, include_contigs
 from nanomotif.binnary.logging import set_logger_config
-from pymethylation_utils.utils import run_methylation_utils
+from pymethylation_utils.utils import run_epimetheus
 
 
 def binnary(args, pl):
@@ -479,9 +479,9 @@ def binnary(args, pl):
     if os.path.isfile(os.path.join(args.out,contig_methylation_file)) and not args.force:
         log.info("motifs-scored-read-methylation.tsv exists. Using existing file! Use --force to override this.")
     elif not os.path.isfile(os.path.join(args.out, contig_methylation_file)) or args.force:
-        log.info(f"Running methylation_utils to create {contig_methylation_file}")
+        log.info(f"Running epimetheus to create {contig_methylation_file}")
         # Create motifs-scored-read-methylation
-        return_code = run_methylation_utils(
+        return_code = run_epimetheus(
             pileup = args.pileup,
             assembly = args.assembly,
             motifs = motifs_in_bin_consensus,
@@ -491,7 +491,7 @@ def binnary(args, pl):
         )
 
         if return_code != 0:
-            log.error("Error running methylation_utils")
+            log.error("Error running epimetheus")
 
 
     log.info("Loading assembly file...")

setup.py

@@ -35,7 +35,7 @@
         "scikit-learn>=1.5.2",
         "networkx>=3.1",
         "pyarrow>=15.0.2",
-        "pymethylation_utils==0.4.0",
+        "pymethylation_utils==0.5.1",
         "hdbscan",
         "Bio>=1.6.2",
         "snakemake>=7.32.4",

tests/binnary/test_utils.py

@@ -1,7 +1,7 @@
 import polars as pl
 import pandas as pd
 import nanomotif.binnary.utils as ut
-from pymethylation_utils.utils import run_methylation_utils
+from pymethylation_utils.utils import run_epimetheus
 from .conftest import MockArgs
 import os
 from pathlib import Path
@@ -31,7 +31,7 @@ def test_split_bin_contig():
 def test_methylation_utils():
     args = MockArgs()
 
-    run_methylation_utils(
+    run_epimetheus(
         pileup = "nanomotif/datasets/geobacillus-plasmids.pileup.bed",
         assembly = "nanomotif/datasets/geobacillus-plasmids.assembly.fasta",
         motifs = ["GATC_m_3", "GATC_a_1"],
@@ -45,7 +45,7 @@ def test_methylation_utils():
 
     res = pl.read_csv(file, separator = "\t")
     print(res.columns)
-    assert res.columns == ["contig",  "median", "N_motif_obs", "mean_read_cov","motif", "mod_type", "mod_position"]
-    assert res.shape == (4, 7), "Shape does not match"
+    assert res.columns == ['contig', 'motif', 'mod_type', 'mod_position', 'median', 'mean_read_cov', 'N_motif_obs', 'motif_occurences_total']
+    assert res.shape == (4, 8), "Shape does not match"