smftools 0.2.1__py3-none-any.whl → 0.2.4__py3-none-any.whl

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")