smftools 0.2.4__py3-none-any.whl → 0.3.0__py3-none-any.whl

smftools/informatics/archived/helpers/archived/modQC.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## modQC
 
 # Direct SMF

smftools/informatics/archived/helpers/archived/modcall.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## modcall
 
 # Direct methylation specific

smftools/informatics/archived/helpers/archived/ohe_batching.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import os
 import anndata as ad
 import numpy as np

smftools/informatics/archived/helpers/archived/ohe_layers_decode.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # ohe_layers_decode
 
 def ohe_layers_decode(adata, obs_names):

smftools/informatics/archived/helpers/archived/one_hot_decode.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # one_hot_decode
 
 # String encodings

smftools/informatics/archived/helpers/archived/one_hot_encode.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # one_hot_encode
 
 def one_hot_encode(sequence, device='auto'):

smftools/informatics/archived/helpers/archived/plot_bed_histograms.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # plot_bed_histograms
 
 def plot_bed_histograms(
@@ -86,6 +88,7 @@ def plot_bed_histograms(
 
     # Clip helper for hist tails
     def _clip_series(s, q=(0.0, 0.995)):
+        """Clip a Series to quantile bounds for plotting."""
         if q is None:
             return s.to_numpy()
         lo = s.quantile(q[0]) if q[0] is not None else s.min()
@@ -109,6 +112,7 @@ def plot_bed_histograms(
 
     # Pagination
     def _sanitize(name: str) -> str:
+        """Sanitize a string for use in filenames."""
         return "".join(ch if ch.isalnum() or ch in "-._" else "_" for ch in name)
 
     cols_per_fig = 4 if include_mapq_quality else 2
@@ -247,4 +251,4 @@ def plot_bed_histograms(
     #     plt.grid(True)
     #     save_name = os.path.join(plotting_directory, f'{bed_basename}_{chrom}_coverage_histogram.png')
     #     plt.savefig(save_name)
-    #     plt.close()
+    #     plt.close()

smftools/informatics/archived/helpers/archived/separate_bam_by_bc.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## separate_bam_by_bc
 
 def separate_bam_by_bc(input_bam, output_prefix, bam_suffix, split_dir):

smftools/informatics/archived/helpers/archived/split_and_index_BAM.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## split_and_index_BAM
 
 def split_and_index_BAM(aligned_sorted_BAM, split_dir, bam_suffix):

smftools/informatics/archived/print_bam_query_seq.py

@@ -1,7 +1,15 @@
+from __future__ import annotations
+
 import pysam
 import sys
 
 def extract_reads(bam_file_path, num_reads=10):
+    """Print sequences for the first N reads in a BAM file.
+
+    Args:
+        bam_file_path: Path to BAM file.
+        num_reads: Number of reads to print.
+    """
     # Open the BAM file
     bam_file = pysam.AlignmentFile(bam_file_path, "rb")
     
@@ -26,4 +34,4 @@ if __name__ == "__main__":
     bam_file_path = sys.argv[1]
     
     # Call the function to extract the first 10 reads
-    extract_reads(bam_file_path)
+    extract_reads(bam_file_path)

smftools/informatics/archived/subsample_fasta_from_bed.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 from pyfaidx import Fasta
 

smftools/informatics/archived/subsample_pod5.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # subsample_pod5
 
 def subsample_pod5(pod5_path, read_name_path, output_directory):