smftools 0.2.1__py3-none-any.whl → 0.2.3__py3-none-any.whl

smftools/informatics/readwrite.py

@@ -1,106 +0,0 @@
-## readwrite ##
-
-######################################################################################################
-## Datetime functionality
-def date_string():
-    """
-    Each time this is called, it returns the current date string
-    """
-    from datetime import datetime
-    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
-    """
-    from datetime import datetime
-    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.
-    """
-    import pandas as pd
-    import anndata as ad
-
-    # 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
-    """
-    import numpy as np
-    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
-    """
-    import os
-    import anndata as ad
-    # Runtime warnings
-    import warnings
-    warnings.filterwarnings('ignore', category=UserWarning, module='anndata')
-    warnings.filterwarnings('ignore', category=FutureWarning, module='anndata')
-    
-    # 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/informatics/subsample_fasta_from_bed.py

@@ -1,47 +0,0 @@
-# subsample_fasta_from_bed
-
-def subsample_fasta_from_bed(input_FASTA, input_bed, output_directory, output_FASTA):
-    """
-    Take a genome-wide FASTA file and a bed file containing coordinate windows of interest. Outputs a subsampled FASTA.
-
-    Parameters:
-        input_FASTA (str): String representing the path to the input FASTA file.
-        input_bed (str): String representing the path to the input BED file.
-        output_directory (str): String representing the path to the output directory for the new FASTA file.
-        output_FASTA (str): Name of the output FASTA.
-    
-    Returns:
-        None
-    """
-    from pyfaidx import Fasta
-    import os
-
-    # Load the FASTA file using pyfaidx
-    fasta = Fasta(input_FASTA)
-
-    output_FASTA_path = os.path.join(output_directory, output_FASTA)
-    
-    # Open the BED file
-    with open(input_bed, 'r') as bed, open(output_FASTA_path, 'w') as out_fasta:
-        for line in bed:
-            # Each line in BED file contains: chrom, start, end (and possibly more columns)
-            fields = line.strip().split()
-            n_fields = len(fields)
-            chrom = fields[0]
-            start = int(fields[1])  # BED is 0-based
-            end = int(fields[2])    # BED is 0-based and end is exclusive
-            if n_fields > 3:
-                description = " ".join(fields[3:])
-            
-            # Check if the chromosome exists in the FASTA file
-            if chrom in fasta:
-                # pyfaidx is 1-based, so convert coordinates accordingly
-                sequence = fasta[chrom][start:end].seq
-                # Write the sequence to the output FASTA file
-                if n_fields > 3:
-                    out_fasta.write(f">{chrom}:{start}-{end}    {description}\n")
-                else:
-                    out_fasta.write(f">{chrom}:{start}-{end}\n")
-                out_fasta.write(f"{sequence}\n")
-            else:
-                print(f"Warning: {chrom} not found in the FASTA file")