smftools 0.1.0__py3-none-any.whl

smftools/readwrite.py

@@ -0,0 +1,109 @@
+## readwrite ##
+
+# Basic I/O
+import os
+# Datetime
+from datetime import datetime
+# Data structures and basic operations
+import math
+import numpy as np
+import pandas as pd
+import anndata as ad
+import scipy.sparse as sp
+
+# Runtime warnings
+import warnings
+warnings.filterwarnings('ignore', category=UserWarning, module='anndata')
+warnings.filterwarnings('ignore', category=FutureWarning, module='anndata')
+
+######################################################################################################
+## Datetime functionality
+def date_string():
+    """
+    Each time this is called, it returns the current date string
+    """
+    current_date = datetime.now()
+    date_string = current_date.strftime("%Y%m%d")
+    date_string = date_string[2:]
+    return date_string
+
+def time_string():
+    """
+    Each time this is called, it returns the current time string
+    """
+    current_time = datetime.now()
+    return current_time.strftime("%H:%M:%S")
+######################################################################################################
+
+######################################################################################################
+## Numpy, Pandas, Anndata functionality
+def adata_to_df(adata, layer=None):
+    """
+    Input: An adata object with a specified layer.
+    Output: A dataframe for the specific layer.
+    """
+    # Extract the data matrix from the given layer
+    if layer:
+        data_matrix = adata.layers[layer]
+    else:
+        data_matrix = adata.X
+    # Extract observation (read) annotations
+    obs_df = adata.obs
+    # Extract variable (position) annotations
+    var_df = adata.var
+    # Convert data matrix and annotations to pandas DataFrames
+    df = pd.DataFrame(data_matrix, index=obs_df.index, columns=var_df.index)
+    return df
+
+def save_matrix(matrix, save_name):
+    """
+    Input: A numpy matrix and a save_name
+    Output: A txt file representation of the data matrix
+    """
+    np.savetxt(f'{save_name}.txt', matrix)
+
+def concatenate_h5ads(output_file, file_suffix='h5ad.gz', delete_inputs=True):
+    """
+    Concatenate all h5ad files in a directory and delete them after the final adata is written out.
+    Input: an output file path relative to the directory in which the function is called
+    """
+    # List all files in the directory
+    files = os.listdir(os.getcwd())
+    # get current working directory
+    cwd = os.getcwd()
+    suffix = file_suffix
+    # Filter file names that contain the search string in their filename and keep them in a list
+    hdfs = [hdf for hdf in files if suffix in hdf]
+    # Sort file list by names and print the list of file names
+    hdfs.sort()
+    print('{0} sample files found: {1}'.format(len(hdfs), hdfs))
+    # Iterate over all of the hdf5 files and concatenate them.
+    final_adata = None
+    for hdf in hdfs:
+        print('{0}: Reading in {1} hdf5 file'.format(time_string(), hdf))
+        temp_adata = ad.read_h5ad(hdf)
+        if final_adata:
+            print('{0}: Concatenating final adata object with {1} hdf5 file'.format(time_string(), hdf))
+            final_adata = ad.concat([final_adata, temp_adata], join='outer', index_unique=None)
+        else:
+            print('{0}: Initializing final adata object with {1} hdf5 file'.format(time_string(), hdf))
+            final_adata = temp_adata
+    print('{0}: Writing final concatenated hdf5 file'.format(time_string()))
+    final_adata.write_h5ad(output_file, compression='gzip')
+
+    # Delete the individual h5ad files and only keep the final concatenated file
+    if delete_inputs:
+        files = os.listdir(os.getcwd())
+        hdfs = [hdf for hdf in files if suffix in hdf]
+        if output_file in hdfs:
+            hdfs.remove(output_file)
+            # Iterate over the files and delete them
+            for hdf in hdfs:
+                try:
+                    os.remove(hdf)
+                    print(f"Deleted file: {hdf}")
+                except OSError as e:
+                    print(f"Error deleting file {hdf}: {e}")
+    else:
+        print('Keeping input files')
+######################################################################################################

smftools-0.1.0.dist-info/METADATA

@@ -0,0 +1,75 @@
+Metadata-Version: 2.3
+Name: smftools
+Version: 0.1.0
+Summary: Single Molecule Footprinting Analysis in Python.
+Project-URL: Source, https://github.com/jkmckenna/smftools
+Author: Joseph McKenna
+Maintainer-email: Joseph McKenna <jkmckenna@berkeley.edu>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: anndata,chromatin-accessibility,machine-learning,nanopore,protein-dna-binding,single-locus,single-molecule-footprinting
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.9
+Requires-Dist: anndata>=0.10.0
+Requires-Dist: biopython>=1.79
+Requires-Dist: cython>=0.29.28
+Requires-Dist: networkx>=3.2
+Requires-Dist: numpy<2,>=1.22.0
+Requires-Dist: pandas>=1.4.2
+Requires-Dist: pomegranate>1.0.0
+Requires-Dist: pysam>=0.19.1
+Requires-Dist: scanpy>=1.9
+Requires-Dist: scikit-learn>=1.0.2
+Requires-Dist: scipy>=1.7.3
+Requires-Dist: seaborn>=0.11
+Requires-Dist: tqdm
+Provides-Extra: base-tests
+Requires-Dist: pytest; extra == 'base-tests'
+Requires-Dist: pytest-cov; extra == 'base-tests'
+Provides-Extra: doc
+Requires-Dist: ipython>=7.20; extra == 'doc'
+Requires-Dist: matplotlib!=3.6.1; extra == 'doc'
+Requires-Dist: myst-nb>=1; extra == 'doc'
+Requires-Dist: myst-parser>=2; extra == 'doc'
+Requires-Dist: nbsphinx>=0.9; extra == 'doc'
+Requires-Dist: readthedocs-sphinx-search; extra == 'doc'
+Requires-Dist: setuptools; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints>=1.25.2; extra == 'doc'
+Requires-Dist: sphinx-book-theme>=1.1.0; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx-design; extra == 'doc'
+Requires-Dist: sphinx>=7; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'doc'
+Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: torch
+Requires-Dist: pomeganate>=1.0.0; extra == 'torch'
+Requires-Dist: torch>=1.9.0; extra == 'torch'
+Provides-Extra: torch-tests
+Requires-Dist: pomeganate>=1.0.0; extra == 'torch-tests'
+Requires-Dist: pytest; extra == 'torch-tests'
+Requires-Dist: pytest-cov; extra == 'torch-tests'
+Requires-Dist: torch>=1.9.0; extra == 'torch-tests'
+Description-Content-Type: text/markdown
+
+# smftools
+A tool for processing raw sequencing data for single molecule footprinting experiments at single genomic loci.
+
+## Dependencies
+The following tools need to be installed and configured:
+1) [Dorado](https://github.com/nanoporetech/dorado) -> For standard/modified basecalling and alignment. Can be attained by downloading and configuring nanopore MinKnow software.
+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

smftools-0.1.0.dist-info/RECORD

@@ -0,0 +1,58 @@
+smftools/__init__.py,sha256=pWcysCXCokCdW4YySaA8BMumZkE56m15otMPG88nQGc,444
+smftools/_settings.py,sha256=a1uYWNBNtQb30cGSdpjeiIMnQV1Fip7IZAQrNzjXR5w,324
+smftools/readwrite.py,sha256=p-K_RYOrM0vDawBTcuCUyuwVzmYwJqNMvhv9fCTLDKE,4159
+smftools/datasets/F1_hybrid_NKG2A_enhander_promoter_GpC_conversion_SMF.h5ad.gz,sha256=q6wJtgFRDln0o20XNCx1qad3lwcdCoylqPN7wskTfI8,2926497
+smftools/datasets/__init__.py,sha256=xkSTlPuakVYVCuRurif9BceNBDt6bsngJvvjI8757QI,142
+smftools/datasets/dCas9_m6A_invitro_kinetics.h5ad.gz,sha256=niOcVHaYY7h3XyvwSkN-V_NMBaRt2vTP5TrJO0CwMCs,8385050
+smftools/datasets/datasets.py,sha256=rAcp7_Raa8Uv95DISj-oACY1fE_5fIfb5Poj-9WVOWo,473
+smftools/informatics/__init__.py,sha256=Bjufdncl978d-tNriuRHX92mjeAO5axjTlZP7iePjms,235
+smftools/informatics/pod5_conversion.py,sha256=m_qNRSNeUndl5KO8PJPMLCOWqcVq-TJSvoyUnJW-UHE,1399
+smftools/informatics/pod5_direct.py,sha256=MGQkpHI2qQuEO0IDFOiXjL0Pq59oC1DwUaIWH7jTHiU,1707
+smftools/informatics/pod5_to_adata.py,sha256=R31bkGbparRGpYpTZ69znQThK1xCGChlf4oP836IC9Y,722
+smftools/informatics/readwrite.py,sha256=p-K_RYOrM0vDawBTcuCUyuwVzmYwJqNMvhv9fCTLDKE,4159
+smftools/informatics/helpers/__init__.py,sha256=ws8Zyxin68L7G5R9Rna_qoBnkSNOaD1ndlcrooV2d-k,1466
+smftools/informatics/helpers/align_BAM.py,sha256=vZpkbI-mUqd6qJaovRhuNM03s816fjd5hNEcfA0oHxo,1414
+smftools/informatics/helpers/binarize_converted_base_identities.py,sha256=rTdk06BmU_bvuE1NOU1LGSQs9ytkl7vQjZcwMbA5Yx0,1409
+smftools/informatics/helpers/canoncall.py,sha256=Ujz0Pkp_wW-XJyb3uB2fzVpB12c2MCOWVTg_uIOQL8c,397
+smftools/informatics/helpers/converted_BAM_to_adata.py,sha256=7tntnkTZpNqS0WTMbO42ksxXqzk9NFpXK0q6uWSqtkM,8593
+smftools/informatics/helpers/count_aligned_reads.py,sha256=Q9iU0zwwNZRn0oOxRl_x5OAF7YgaRkSpQBojaBccQsI,1814
+smftools/informatics/helpers/extract_base_identities.py,sha256=nrQy8cUyOA2C8cKKL6SpZ97U0ZGhChw8Qdk0BwuxIT4,2406
+smftools/informatics/helpers/extract_mods.py,sha256=IQdpQxh_2NStKK4kIVKa8UAcV-fVJSs_bzB3JLe0Jx4,1602
+smftools/informatics/helpers/find_conversion_sites.py,sha256=aer63p2JHqaoB3wSK9xqpSjow7w7UyrMSJ06aKTQSiQ,3208
+smftools/informatics/helpers/generate_converted_FASTA.py,sha256=xHjspkeCiSKjqb6zUrjCG13OKW597LJ4_w33tg-wFok,3006
+smftools/informatics/helpers/get_native_references.py,sha256=wx_RXnPwj0NGp7Tx1_hXyO8ZzQJHZwa0b3a6r3266FY,976
+smftools/informatics/helpers/informatics.py,sha256=gKb2ZJ_LcAeEXuQqn9e-QDF_sS4tMpMTr2vZlqa7n54,14572
+smftools/informatics/helpers/load_adata.py,sha256=DhvYYqO9VLsZqhL1WjN9sd-e3fgvdXGlgTP18z1h0L0,33654
+smftools/informatics/helpers/load_experiment_config.py,sha256=boF524jZZKzBjc2yvAiMYvhM4OW_efXSbwU-nINKDdg,607
+smftools/informatics/helpers/make_dirs.py,sha256=UxghbuquyXgDD-H24Ghf1B7Kfpdt04NgMs8GE6zSJ3U,475
+smftools/informatics/helpers/make_modbed.py,sha256=m1lQUbw0W63YjiM_Tmy6QOL3GkHgvSuCrkX2Bo8sCco,741
+smftools/informatics/helpers/modQC.py,sha256=C-WVaoLN7Dxh--JcWa4UXzhwFpf0AXrFA99IsxfVXwo,770
+smftools/informatics/helpers/modcall.py,sha256=f41SkaXi2fYgv7B0oAFwj-9CZ0XVhvzWHfe977rT0wQ,493
+smftools/informatics/helpers/modkit_extract_to_adata.py,sha256=TvIHDXWTO2QxArGyIU3w-dQBVyq0rQ1A4iMvV9Rb_7A,24407
+smftools/informatics/helpers/one_hot_encode.py,sha256=jxfTNREED0YhdvwhVmRrt2BZUfiOrOUURVSOVtGypns,439
+smftools/informatics/helpers/separate_bam_by_bc.py,sha256=AFT-v0XXuW2rRYG6FC-8gulhAA6a4YGAa0UEuMDlimc,1235
+smftools/informatics/helpers/split_and_index_BAM.py,sha256=HqPAy5YxK0jokCWCUlUIWSLf2n-Gubkge-xxYfX4XLE,755
+smftools/plotting/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+smftools/preprocessing/__init__.py,sha256=ngs4XYcd9gSXwSa-gi1pWMblCRJ_uZo5MMkg5vuhDOU,1438
+smftools/preprocessing/append_C_context.py,sha256=sfHiV3gBOum3KyZ6wFOCUcDUieW9rra3hKFkWEb8wmk,2063
+smftools/preprocessing/binarize_on_Youden.py,sha256=CO0KnxxHmCwq7tlrBh7BuY0_6SEacR7NwRhkwaWoVUg,2056
+smftools/preprocessing/binary_layers_to_ohe.py,sha256=zahq1YcgAeva-b1CcEVaBK4XaNmMgE6IpfiedYepI5k,876
+smftools/preprocessing/calculate_complexity.py,sha256=H4j0mCWL-jFWZ8UoTGa5lNEcqByfwIDtlsJrpNRNkg4,2751
+smftools/preprocessing/calculate_converted_read_methylation_stats.py,sha256=ZIOKGkbWI15RzpnfgWU4MUXFz3LlUjL_yjodGrye8-A,2626
+smftools/preprocessing/calculate_coverage.py,sha256=Q-RjTqbYt9jc-Axk807_h0m7_oDFdewrO805FQARLUA,1852
+smftools/preprocessing/calculate_pairwise_hamming_distances.py,sha256=l0IYlWu9RCDq4R2pJm_qGXN_RyFkIuah9fFLvg1Hti0,843
+smftools/preprocessing/calculate_position_Youden.py,sha256=FUSsrhp8L8TLoJaX2cSl8u1phNbYpTRJfVqsrwMOWgY,6008
+smftools/preprocessing/calculate_read_length_stats.py,sha256=kKcEw4zS-GnJ2nyC5c24YVMY2oBmxmcxjPWLGnrkwws,1711
+smftools/preprocessing/clean_NaN.py,sha256=HCRX_nA6H3o7CysCa6yxN07xQEoh6LvdkX7aAYqSKR8,1024
+smftools/preprocessing/filter_converted_reads_on_methylation.py,sha256=krqDb6TNjQx4IICXbEQ8SDcaSjrWZ-9ChtaEiIxU5KY,962
+smftools/preprocessing/filter_reads_on_length.py,sha256=-tXMIpg8Mx8GskCfjBy0ZBczuJRTZdyuSZtDyb6KDJs,1737
+smftools/preprocessing/invert_adata.py,sha256=vpR0jynLODhE8mpiHZQIv1XUY9pd7cEG0ujC-GArXIE,616
+smftools/preprocessing/mark_duplicates.py,sha256=Qd1fluCHkL7ZAY37wGmBe40HwkRipOkbDAp6lnoLU9I,6818
+smftools/preprocessing/min_non_diagonal.py,sha256=o79E5xy-aO-cSwN5dUVi5oj8_EfQBDPcj1D0_7fvk1Q,644
+smftools/preprocessing/preprocessing.py,sha256=4mLT09A7vwRZ78FHmuwtv38mH9TQ9qrZc_WjHRhhkIw,34379
+smftools/preprocessing/remove_duplicates.py,sha256=sgdRjZSLakocTRwAukdp1RpFhODbeOjNN_EWZkTshAc,395
+smftools/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+smftools-0.1.0.dist-info/METADATA,sha256=Loh3iFQgPLn6Xe_WdbeATlGiMqggFaYJOqgwf5e8WRI,3422
+smftools-0.1.0.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+smftools-0.1.0.dist-info/licenses/LICENSE,sha256=F8LwmL6vMPddaCt1z1S83Kh_OZv50alTlY7BvVx1RXw,1066
+smftools-0.1.0.dist-info/RECORD,,

smftools-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.25.0
+Root-Is-Purelib: true
+Tag: py3-none-any

smftools-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 jkmckenna
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.