smftools 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

{smftools-0.1.1.dist-info → smftools-0.1.3.dist-info}/METADATA

@@ -1,8 +1,9 @@
 Metadata-Version: 2.3
 Name: smftools
-Version: 0.1.1
+Version: 0.1.3
 Summary: Single Molecule Footprinting Analysis in Python.
 Project-URL: Source, https://github.com/jkmckenna/smftools
+Project-URL: Documentation, https://smftools.readthedocs.io/
 Author: Joseph McKenna
 Maintainer-email: Joseph McKenna <jkmckenna@berkeley.edu>
 License-Expression: MIT
@@ -31,6 +32,7 @@ Requires-Dist: numpy<2,>=1.22.0
 Requires-Dist: pandas>=1.4.2
 Requires-Dist: pod5>=0.1.21
 Requires-Dist: pomegranate>1.0.0
+Requires-Dist: pyfaidx>=0.8.0
 Requires-Dist: pysam>=0.19.1
 Requires-Dist: scanpy>=1.9
 Requires-Dist: scikit-learn>=1.0.2
@@ -38,9 +40,6 @@ Requires-Dist: scipy>=1.7.3
 Requires-Dist: seaborn>=0.11
 Requires-Dist: torch>=1.9.0
 Requires-Dist: tqdm
-Provides-Extra: base-tests
-Requires-Dist: pytest; extra == 'base-tests'
-Requires-Dist: pytest-cov; extra == 'base-tests'
 Provides-Extra: docs
 Requires-Dist: ipython>=7.20; extra == 'docs'
 Requires-Dist: matplotlib!=3.6.1; extra == 'docs'
@@ -56,13 +55,16 @@ Requires-Dist: sphinx-design; extra == 'docs'
 Requires-Dist: sphinx>=7; extra == 'docs'
 Requires-Dist: sphinxcontrib-bibtex; extra == 'docs'
 Requires-Dist: sphinxext-opengraph; extra == 'docs'
+Provides-Extra: tests
+Requires-Dist: pytest; extra == 'tests'
+Requires-Dist: pytest-cov; extra == 'tests'
 Description-Content-Type: text/markdown
 
 [![PyPI](https://img.shields.io/pypi/v/smftools.svg)](https://pypi.org/project/smftools)
 [![Docs](https://readthedocs.org/projects/smftools/badge/?version=latest)](https://smftools.readthedocs.io/en/latest/?badge=latest)
 
 # smftools
-A Python tool for processing raw sequencing data derived from single molecule footprinting experiments into [anndata](https://anndata.readthedocs.io/en/latest/) objects. Additional functionality for preprocessing, analysis, and visualization. Data structures are compatible with analyses developed within the [scverse](https://github.com/scverse) project, including [scanpy](https://github.com/scverse/scanpy) and [scvi-tools](https://github.com/scverse/scvi-tools).
+A Python tool for processing raw sequencing data derived from single molecule footprinting experiments into [anndata](https://anndata.readthedocs.io/en/latest/) objects. Additional functionality for preprocessing, analysis, and visualization.
 
 ## Philosophy
 While most genomic data structures handle low-coverage data (<100X) along large references, smftools prioritizes high-coverage data (scalable to at least 1 million X coverage) of a few genomic loci at a time. This enables efficient data storage, rapid data operations, hierarchical metadata handling, seamless integration with various machine-learning packages, and ease of visualization. Furthermore, functionality is modularized, enabling analysis sessions to be saved, reloaded, and easily shared with collaborators. Analyses are centered around the [anndata](https://anndata.readthedocs.io/en/latest/) object, and are heavily inspired by the work conducted within the single-cell genomics community.
@@ -73,10 +75,14 @@ The following CLI tools need to be installed and configured before using the inf
 2) [Samtools](https://github.com/samtools/samtools) -> For working with SAM/BAM files
 3) [Minimap2](https://github.com/lh3/minimap2) -> The aligner used by Dorado
 4) [Modkit](https://github.com/nanoporetech/modkit) -> Extracting summary statistics and read level methylation calls from modified BAM files
+5) [Bedtools](https://github.com/arq5x/bedtools2) -> For generating Bedgraphs from BAM alignment files.
+6) [BedGraphToBigWig](https://genome.ucsc.edu/goldenPath/help/bigWig.html) -> For converting BedGraphs to BigWig files for IGV sessions.
 
 ## Modules
-- Informatics: Processes raw SMF data coming from Nanopore POD5 files, BAM files, or FASTQ files and organizes it into an AnnData object.
-- Preprocessing: Filters the AnnData object on read length, total methylation, and a variety of QC metrics.
+### Informatics: Processes raw Nanopore/Illumina data from SMF experiments into an AnnData object.
+![](docs/source/_static/smftools_informatics_diagram.png)
+### Preprocessing: Appends QC metrics to the AnnData object and perfroms filtering.
+![](docs/source/_static/smftools_preprocessing_diagram.png)
 - Tools: Appends various analyses to the AnnData object.
 - Plotting: Visualization of analyses stored within the AnnData object.
 

smftools-0.1.3.dist-info/RECORD

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smftools/informatics/basecalls_to_adata.py

@@ -1,42 +0,0 @@
-## basecalls_to_adata
-
-def basecalls_to_adata(config_path):
-    """
-    High-level function to call for loading basecalled SMF data from a BAM file into an adata object. Also works with FASTQ for conversion SMF.
-
-    Parameters:
-        config_path (str): A string representing the file path to the experiment configuration csv file.
-
-    Returns:
-        None
-    """
-    from .helpers import LoadExperimentConfig, make_dirs
-    import os
-    bam_suffix = '.bam' # If different, change from here.
-    split_dir = 'split_BAMs' # If different, change from here.
-    strands = ['bottom', 'top'] # If different, change from here. Having both listed generally doesn't slow things down too much.
-    conversions = ['unconverted'] # The name to use for the unconverted files. If different, change from here.
-
-    # Load experiment config parameters into global variables
-    experiment_config = LoadExperimentConfig(config_path)
-    var_dict = experiment_config.var_dict
-    for key, value in var_dict.items():
-        globals()[key] = value
-
-    split_path = os.path.join(output_directory, split_dir)
-    make_dirs([output_directory, split_path])
-    os.chdir(output_directory)
-
-    conversions += conversion_types
-
-    if smf_modality == 'conversion':
-        from .bam_conversion import bam_conversion
-        bam_conversion(fasta, output_directory, conversions, strands, basecalled_path, split_path, mapping_threshold, experiment_name, bam_suffix)
-    elif smf_modality == 'direct':
-        if bam_suffix in basecalled_path:
-            from .bam_direct import bam_direct
-            bam_direct(fasta, output_directory, mod_list, thresholds, basecalled_path, split_path, mapping_threshold, experiment_name, bam_suffix, batch_size)
-        else:
-            print('basecalls_to_adata function only work with the direct modality when the input filetype is BAM and not FASTQ.')
-    else:
-        print("Error")

smftools/informatics/pod5_conversion.py

@@ -1,53 +0,0 @@
-## pod5_conversion
-
-def pod5_conversion(fasta, output_directory, conversion_types, strands, model, pod5_dir, split_dir, barcode_kit, mapping_threshold, experiment_name, bam_suffix):
-    """
-    Converts a POD5 file from a nanopore conversion SMF experiment to an adata object.
-
-    Parameters:
-        fasta (str): File path to the reference genome to align to.
-        output_directory (str): A file path to the directory to output all the analyses.
-        conversion_type (list): A list of strings of the conversion types to use in the analysis.
-        strands (list): A list of converstion strands to use in the experiment.
-        model (str): a string representing the file path to the dorado basecalling model.
-        pod5_dir (str): a string representing the file path to the experiment directory containing the POD5 files.
-        split_dir (str): A string representing the file path to the directory to split the BAMs into.
-        barcode_kit (str): A string representing the barcoding kit used in the experiment.
-        mapping_threshold (float): A value in between 0 and 1 to threshold the minimal fraction of aligned reads which map to the reference region. References with values above the threshold are included in the output adata.
-        experiment_name (str): A string to provide an experiment name to the output adata file.
-        bam_suffix (str): A suffix to add to the bam file.
-
-    Returns:
-        None
-    """
-    from .helpers import align_and_sort_BAM, canoncall, converted_BAM_to_adata, generate_converted_FASTA, split_and_index_BAM
-    import os
-    model_basename = os.path.basename(model)
-    model_basename = model_basename.replace('.', '_')
-    bam=f"{output_directory}/{model_basename}_canonical_basecalls"
-    aligned_BAM=f"{bam}_aligned"
-    aligned_sorted_BAM=f"{aligned_BAM}_sorted"
-
-    os.chdir(output_directory)
-    
-    # 1) Convert FASTA file
-    fasta_basename = os.path.basename(fasta)
-    converted_FASTA_basename = fasta_basename.split('.fa')[0]+'_converted.fasta'
-    converted_FASTA = os.path.join(output_directory, converted_FASTA_basename)
-    if os.path.exists(converted_FASTA):
-        print(converted_FASTA + ' already exists. Using existing converted FASTA.')
-    else:
-        generate_converted_FASTA(fasta, conversion_types, strands, converted_FASTA)
-
-    # 2) Basecall from the input POD5 to generate a singular output BAM
-    canoncall(model, pod5_dir, barcode_kit, bam, bam_suffix)
-
-    # 3) Align the BAM to the converted reference FASTA and sort the bam on positional coordinates. Also make an index and a bed file of mapped reads
-    input_BAM = bam + bam_suffix
-    align_and_sort_BAM(converted_FASTA, input_BAM, bam_suffix, output_directory)
-
-    ### 4) Split the aligned and sorted BAM files by barcode (BC Tag) into the split_BAM directory###
-    split_and_index_BAM(aligned_sorted_BAM, split_dir, bam_suffix)
-
-    # 5) Take the converted BAM and load it into an adata object. 
-    converted_BAM_to_adata(converted_FASTA, split_dir, mapping_threshold, experiment_name, conversion_types, bam_suffix)

smftools/informatics/pod5_direct.py

@@ -1,55 +0,0 @@
-## pod5_direct
-
-def pod5_direct(fasta, output_directory, mod_list, model, thresholds, pod5_dir, split_dir, barcode_kit, mapping_threshold, experiment_name, bam_suffix, batch_size):
-    """
-    Converts a POD5 file from a nanopore native SMF experiment to an adata object.
-
-    Parameters:
-        fasta (str): File path to the reference genome to align to.
-        output_directory (str): A file path to the directory to output all the analyses.
-        mod_list (list): A list of strings of the modification types to use in the analysis.
-        model (str): a string representing the file path to the dorado basecalling model.
-        thresholds (list): A list of floats to pass for call thresholds.
-        pod5_dir (str): a string representing the file path to the experiment directory containing the POD5 files.
-        split_dir (str): A string representing the file path to the directory to split the BAMs into.
-        barcode_kit (str): A string representing the barcoding kit used in the experiment.
-        mapping_threshold (float): A value in between 0 and 1 to threshold the minimal fraction of aligned reads which map to the reference region. References with values above the threshold are included in the output adata.
-        experiment_name (str): A string to provide an experiment name to the output adata file.
-        bam_suffix (str): A suffix to add to the bam file.
-        batch_size (int): An integer number of TSV files to analyze in memory at once while loading the final adata object.
-
-    Returns:
-        None   
-    """
-    from .helpers import align_and_sort_BAM, extract_mods, make_modbed, modcall, modkit_extract_to_adata, modQC, split_and_index_BAM, make_dirs
-    import os
-    model_basename = os.path.basename(model)
-    model_basename = model_basename.replace('.', '_')
-    mod_string = "_".join(mod_list)
-    bam=f"{output_directory}/{model_basename}_{mod_string}_calls"
-    aligned_BAM=f"{bam}_aligned"
-    aligned_sorted_BAM=f"{aligned_BAM}_sorted"
-    mod_bed_dir=f"{output_directory}/split_mod_beds"
-    mod_tsv_dir=f"{output_directory}/split_mod_tsvs"
-
-    make_dirs([mod_bed_dir, mod_tsv_dir])
-
-    aligned_sorted_output = aligned_sorted_BAM + bam_suffix
-    mod_map = {'6mA': '6mA', '5mC_5hmC': '5mC'}
-    mods = [mod_map[mod] for mod in mod_list]
-
-    os.chdir(output_directory)
-
-    # 1) Basecall using dorado
-    modcall(model, pod5_dir, barcode_kit, mod_list, bam, bam_suffix)
-    # 2) Align the BAM to the reference FASTA. Also make an index and a bed file of mapped reads
-    input_BAM = bam + bam_suffix
-    align_and_sort_BAM(fasta, input_BAM, bam_suffix, output_directory)
-    # 3) Split the aligned and sorted BAM files by barcode (BC Tag) into the split_BAM directory
-    split_and_index_BAM(aligned_sorted_BAM, split_dir, bam_suffix)
-    # 4) Using nanopore modkit to work with modified BAM files ###
-    modQC(aligned_sorted_output, thresholds) # get QC metrics for mod calls
-    make_modbed(aligned_sorted_output, thresholds, mod_bed_dir) # Generate bed files of position methylation summaries for every sample
-    extract_mods(thresholds, mod_tsv_dir, split_dir, bam_suffix) # Extract methylations calls for split BAM files into split TSV files
-    #5 Load the modification data from TSVs into an adata object
-    modkit_extract_to_adata(fasta, aligned_sorted_output, mapping_threshold, experiment_name, mods, batch_size)

smftools/informatics/pod5_to_adata.py

@@ -1,40 +0,0 @@
-## pod5_to_adata
-
-def pod5_to_adata(config_path):
-    """
-    High-level function to call for converting raw sequencing data to an adata object.
-
-    Parameters:
-        config_path (str): A string representing the file path to the experiment configuration csv file.
-
-    Returns:
-        None
-    """
-    from .helpers import LoadExperimentConfig, make_dirs
-    import os
-    bam_suffix = '.bam' # If different, change from here.
-    split_dir = 'split_BAMs' # If different, change from here.
-    strands = ['bottom', 'top'] # If different, change from here. Having both listed generally doesn't slow things down too much.
-    conversions = ['unconverted'] # The name to use for the unconverted files. If different, change from here.
-
-    # Load experiment config parameters into global variables
-    experiment_config = LoadExperimentConfig(config_path)
-    var_dict = experiment_config.var_dict
-    for key, value in var_dict.items():
-        globals()[key] = value
-
-    conversions += conversion_types
-
-    split_path = os.path.join(output_directory, split_dir)
-    make_dirs([output_directory, split_path])
-    os.chdir(output_directory)
-
-    if smf_modality == 'conversion':
-        from .pod5_conversion import pod5_conversion
-        pod5_conversion(fasta, output_directory, conversions, strands, model, pod5_dir, split_path, barcode_kit, mapping_threshold, experiment_name, bam_suffix)
-    elif smf_modality == 'direct':
-        from .pod5_direct import pod5_direct
-        thresholds = [filter_threshold, m6A_threshold, m5C_threshold, hm5C_threshold]
-        pod5_direct(fasta, output_directory, mod_list, model, thresholds, pod5_dir, split_path, barcode_kit, mapping_threshold, experiment_name, bam_suffix, batch_size)
-    else:
-        print("Error")

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