Issue_4

Adding the code for Issue_4 as well as the nextflow workflow

src/primingprob/cli_priming_prob.py

+"""Command-line interface client."""
+import argparse
+import os
+from pathlib import Path
+import sys
+from src.primingprob.priming_prob import Probability as Pbt
+
+
+def parse_args():
+    """Parse CLI arguments.
+
+    Returns:
+        Parsed CLI arguments.
+    """
+    parser = argparse.ArgumentParser(
+        description="RIblast input",
+        add_help=False,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+
+    parser.add_argument(
+        'input_file',
+        type=lambda p: Path(p).absolute(),
+        metavar="PATH",
+        help="path to energy-file",
+    )
+
+    parser.add_argument(
+        'fasta_file',
+        type=lambda p: Path(p).absolute(),
+        metavar="PATH",
+        help="path to fasta-file",
+    )
+
+    parser.add_argument(
+        'output_file',
+        type=lambda p: Path(p).absolute(),
+        metavar="PATH",
+        help="path to output-file",
+    )
+
+    return parser.parse_args()
+
+
+def main():
+    """Start priming_prob.py."""
+    args = parse_args()
+
+    if os.path.exists(args.input_file) and os.path.exists(args.fasta_file):  # pragma: no cover
+        paradata = Pbt.inter_para(args.input_file)
+        Pbt.inter_prob(paradata, args.fasta_file, args.output_file)
+
+    if not os.path.exists(args.input_file) and os.path.exists(args.fasta_file):  # pragma: no cover
+        sys.exit("Path to input-file does not exist")
+
+
+def init():
+    """Entry point for CLI executable."""
+    if __name__ == '__main__':
+        main()
+
+
+init()