From dd17df09d938510e094cfdbcad6ccece3346b40f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= <gordon@koehn.net>
Date: Thu, 14 Nov 2024 16:33:04 +0100
Subject: [PATCH] Remove sinlge sample file

---
 scripts/vp_one_sample.py | 64 ----------------------------------------
 1 file changed, 64 deletions(-)
 delete mode 100644 scripts/vp_one_sample.py

diff --git a/scripts/vp_one_sample.py b/scripts/vp_one_sample.py
deleted file mode 100644
index a3edcc8..0000000
--- a/scripts/vp_one_sample.py
+++ /dev/null
@@ -1,64 +0,0 @@
-"""Process a single BAM file."""
-
-from __future__ import annotations
-
-import logging
-from pathlib import Path
-
-import click
-
-from sr2silo.convert import bam_to_sam
-from sr2silo.process import pair_normalize_reads
-from sr2silo.translation import translate
-
-logging.basicConfig(level=logging.INFO)
-
-
-@click.command()
-@click.option(
-    "--file_path",
-    type=click.Path(exists=True),
-    required=True,
-    help="Path to the input BAM file.",
-)
-@click.option(
-    "--output_dir",
-    type=click.Path(),
-    required=True,
-    help="Directory to save the output files.",
-)
-def process_file(file_path, output_dir):
-    """Process a single BAM file.
-
-    Args:
-        file_path: Path to the input BAM file.
-        output_dir: Directory to save the output files.
-
-    Returns:
-        Full output of nextclade translation.
-        and currently the insertions and normalised reads.
-    """
-    directory = Path(file_path).parent
-    result_dir = Path(output_dir)
-    result_dir.mkdir(parents=True, exist_ok=True)
-    logging.info(f"Processing file: {file_path}")
-
-    # Convert BAM to SAM
-    logging.info(f"Converting BAM to SAM: {file_path}")
-    bam_file = Path(file_path)
-    sam_data = bam_to_sam(bam_file)
-
-    # Process SAM to FASTA
-    logging.info(f"Processing SAM to FASTA: {file_path}")
-    fasta_file = result_dir / "normalized_reads.fasta"
-    insertions_file = result_dir / "normalized_insertions.txt"
-    pair_normalize_reads(sam_data, fasta_file, insertions_file)
-
-    # Translate nucleotides to amino acids
-    logging.info(f"Translating nucleotides to amino acids: {file_path}")
-    nextclade_reference = "nextstrain/sars-cov-2/wuhan-hu-1/orfs"
-    translate([fasta_file], result_dir, nextclade_reference)
-
-
-if __name__ == "__main__":
-    process_file()