smftools 0.1.7__py3-none-any.whl → 0.2.3__py3-none-any.whl

smftools/informatics/archived/subsample_fasta_from_bed.py

@@ -0,0 +1,49 @@
+from pathlib import Path
+from pyfaidx import Fasta
+
+def subsample_fasta_from_bed(
+    input_FASTA: str | Path,
+    input_bed: str | Path,
+    output_directory: str | Path,
+    output_FASTA: str | Path
+) -> None:
+    """
+    Take a genome-wide FASTA file and a BED file containing
+    coordinate windows of interest. Outputs a subsampled FASTA.
+    """
+
+    # Normalize everything to Path
+    input_FASTA = Path(input_FASTA)
+    input_bed = Path(input_bed)
+    output_directory = Path(output_directory)
+    output_FASTA = Path(output_FASTA)
+
+    # Ensure output directory exists
+    output_directory.mkdir(parents=True, exist_ok=True)
+
+    output_FASTA_path = output_directory / output_FASTA
+
+    # Load the FASTA file using pyfaidx
+    fasta = Fasta(str(input_FASTA))   # pyfaidx requires string paths
+
+    # Open BED + output FASTA
+    with input_bed.open("r") as bed, output_FASTA_path.open("w") as out_fasta:
+        for line in bed:
+            fields = line.strip().split()
+            chrom = fields[0]
+            start = int(fields[1]) # BED is 0-based
+            end   = int(fields[2]) # BED is 0-based and end is exclusive
+            desc  = " ".join(fields[3:]) if len(fields) > 3 else ""
+
+            if chrom not in fasta:
+                print(f"Warning: {chrom} not found in FASTA")
+                continue
+
+            # pyfaidx is 1-based indexing internally, but [start:end] works with BED coords
+            sequence = fasta[chrom][start:end].seq
+
+            header = f">{chrom}:{start}-{end}"
+            if desc:
+                header += f"    {desc}"
+
+            out_fasta.write(f"{header}\n{sequence}\n")