smftools 0.2.5__py3-none-any.whl → 0.3.1__py3-none-any.whl

smftools/informatics/archived/bam_conversion.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## bam_conversion
 
 def bam_conversion(fasta, output_directory, conversion_types, strands, basecalled_path, split_dir, mapping_threshold, experiment_name, bam_suffix):

smftools/informatics/archived/bam_direct.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## bam_direct
 
 def bam_direct(fasta, output_directory, mod_list, thresholds, bam_path, split_dir, mapping_threshold, experiment_name, bam_suffix, batch_size):

smftools/informatics/archived/basecall_pod5s.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # basecall_pod5s
 
 def basecall_pod5s(config_path):

smftools/informatics/archived/basecalls_to_adata.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## basecalls_to_adata
 
 def basecalls_to_adata(config_path):

smftools/informatics/archived/conversion_smf.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## conversion_smf
 
 def conversion_smf(fasta, output_directory, conversion_types, strands, model_dir, model, input_data_path, split_dir, barcode_kit, mapping_threshold, experiment_name, bam_suffix, basecall, barcode_both_ends, trim, device, make_bigwigs, threads, input_already_demuxed):

smftools/informatics/archived/deaminase_smf.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 
 def deaminase_smf(fasta, output_directory, conversion_types, strands, model_dir, model, input_data_path, split_dir, barcode_kit, mapping_threshold, experiment_name, bam_suffix, basecall, barcode_both_ends, trim, device, make_bigwigs, threads, input_already_demuxed):
     """

smftools/informatics/archived/direct_smf.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## direct_smf
 
 def direct_smf(fasta, output_directory, mod_list, model_dir, model, thresholds, input_data_path, split_dir, barcode_kit, mapping_threshold, experiment_name, bam_suffix, batch_size, basecall, barcode_both_ends, trim, device, make_bigwigs, skip_unclassified, delete_batch_hdfs, threads):

smftools/informatics/archived/fast5_to_pod5.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 import subprocess
 from typing import Union, List

smftools/informatics/archived/helpers/archived/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # from .align_and_sort_BAM import align_and_sort_BAM
 # from .aligned_BAM_to_bed import aligned_BAM_to_bed
 # from .bam_qc import bam_qc

smftools/informatics/archived/helpers/archived/align_and_sort_BAM.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 import os
 import subprocess

smftools/informatics/archived/helpers/archived/aligned_BAM_to_bed.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 def aligned_BAM_to_bed(aligned_BAM, out_dir, fasta, make_bigwigs, threads=None):
     """
     Takes an aligned BAM as input and writes a BED file of reads as output.

smftools/informatics/archived/helpers/archived/bed_to_bigwig.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 import pybedtools
 import pyBigWig

smftools/informatics/archived/helpers/archived/canoncall.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## canoncall
 
 # Conversion SMF specific

smftools/informatics/archived/helpers/archived/converted_BAM_to_adata.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## converted_BAM_to_adata
 
 def converted_BAM_to_adata(converted_FASTA, split_dir, mapping_threshold, experiment_name, conversion_types, bam_suffix):

smftools/informatics/archived/helpers/archived/count_aligned_reads.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## count_aligned_reads
 
 # General

smftools/informatics/archived/helpers/archived/demux_and_index_BAM.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## demux_and_index_BAM
 
 def demux_and_index_BAM(aligned_sorted_BAM, split_dir, bam_suffix, barcode_kit, barcode_both_ends, trim, fasta, make_bigwigs, threads):

smftools/informatics/archived/helpers/archived/extract_base_identities.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 def extract_base_identities(bam_file, chromosome, positions, max_reference_length, sequence):
     """
     Efficiently extracts base identities from mapped reads with reference coordinates.

smftools/informatics/archived/helpers/archived/extract_mods.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## extract_mods
 
 def extract_mods(thresholds, mod_tsv_dir, split_dir, bam_suffix, skip_unclassified=True, modkit_summary=False, threads=None):

smftools/informatics/archived/helpers/archived/extract_read_features_from_bam.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # extract_read_features_from_bam
 
 def extract_read_features_from_bam(bam_file_path):

smftools/informatics/archived/helpers/archived/extract_read_lengths_from_bed.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # extract_read_lengths_from_bed
 
 def extract_read_lengths_from_bed(file_path):

smftools/informatics/archived/helpers/archived/extract_readnames_from_BAM.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # extract_readnames_from_BAM
 
 def extract_readnames_from_BAM(aligned_BAM):

smftools/informatics/archived/helpers/archived/find_conversion_sites.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 def find_conversion_sites(fasta_file, modification_type, conversions, deaminase_footprinting=False):
     """
     Finds genomic coordinates of modified bases (5mC or 6mA) in a reference FASTA file.

smftools/informatics/archived/helpers/archived/generate_converted_FASTA.py

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

smftools/informatics/archived/helpers/archived/get_chromosome_lengths.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # get_chromosome_lengths
 
 def get_chromosome_lengths(fasta):

smftools/informatics/archived/helpers/archived/get_native_references.py

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

smftools/informatics/archived/helpers/archived/index_fasta.py

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

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

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 ## fasta_module
 from .. import readwrite
 # bioinformatic operations

smftools/informatics/archived/helpers/archived/load_adata.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 # load_adata
 ######################################################################################################
 # Archived helper; legacy imports removed for syntax compatibility.

smftools/informatics/archived/helpers/archived/make_modbed.py

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

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(

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

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import pysam
 import sys
 

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):