Fixed CLI argument issue

term_frag_sel/cli.py

@@ -10,6 +10,13 @@ import pandas as pd  # type: ignore
 from term_frag_sel.fragmentation import fragmentation
 from term_frag_sel.utils import check_positive, check_prob
 
+logging.basicConfig(
+    format='[%(asctime)s: %(levelname)s] %(message)s \
+        (module "%(module)s")',
+    level=logging.INFO,
+)
+logger = logging.getLogger("main")
+
 
 def main(args: argparse.Namespace):
     """Use CLI arguments to fragment sequences and output text file \
@@ -18,6 +25,9 @@ def main(args: argparse.Namespace):
     Args:
         args (parser): list of arguments from CLI.
     """
+    if not isinstance(args, argparse.Namespace):
+        raise TypeError("Input should be argparse.Namespace")
+
     # Create or wipe output file
     with open(args.output, "w", encoding="utf-8") as _:
         pass
@@ -26,17 +36,16 @@ def main(args: argparse.Namespace):
     fasta, seq_counts = file_validation(args.fasta, args.counts, args.sep)
 
     logger.info("Fragmentation of %s...", args.fasta)
-    fasta_parse = {}
-    for record in fasta:
-        fasta_parse[record.id] = record.seq
-    splits = np.arange(0, len(list(fasta_parse))+args.size, args.size)
+    splits = np.arange(0, len(list(fasta))+args.size, args.size)
 
+    nuc_probs = {'A': args.a_prob, 'T': args.t_prob,
+                 'G': args.g_prob, 'C': args.c_prob}
     for i, split in enumerate(splits):
-        fasta_dict = fasta_parse[split:splits[i+1]]
+        fasta_dict = fasta[split:splits[i+1]]
         term_frags = fragmentation(fasta_dict, seq_counts,
+                                   nuc_probs,
                                    args.mean, args.std,
-                                   args.A_prob, args.T_prob,
-                                   args.G_prob, args.C_prob)
+                                   )
 
         logger.info("Writing batch %s sequences to %s...", i, args.output)
         with open(args.output, 'a', encoding="utf-8") as out_file:
@@ -55,24 +64,32 @@ def file_validation(fasta_file: str,
         sep (str): Separator for counts file.
 
     Returns:
-        tuple: fasta and sequence counts variables
+        tuple: fasta dict and sequence counts pd.DataFrame
     """
+    fasta_dict = {}
     with open(fasta_file, "r", encoding="utf-8") as handle:
-        fasta = SeqIO.parse(handle, "fasta")
-    if not any(fasta):
-        raise ValueError("Input FASTA file is either empty or \
-            incorrect file type.")
+        fasta_sequences = SeqIO.parse(handle, "fasta")
+
+        if not any(fasta_sequences):
+            raise ValueError("Input FASTA file is either empty or \
+                incorrect file type.")
+
+        for record in fasta_sequences:
+            fasta_dict[record.id] = str(record.seq).upper()
 
     count_path = Path(counts_file)
     if not count_path.is_file():
-        logger.exception("Input counts file does not exist or isn't a file.")
+        raise FileNotFoundError("Input counts file does not exist or \
+            isn't a file.")
+
+    if sep == ",":
+        seq_counts = pd.read_csv(counts_file, names=["seqID", "count"])
+        seq_counts = seq_counts.astype({"seqID": str})
     else:
-        if sep == ",":
-            seq_counts = pd.read_csv(counts_file, names=["seqID", "count"])
-        else:
-            seq_counts = pd.read_table(counts_file, names=["seqID", "count"])
+        seq_counts = pd.read_table(counts_file, names=["seqID", "count"])
+        seq_counts = seq_counts.astype({"seqID": str})
 
-    return fasta, seq_counts
+    return fasta_dict, seq_counts
 
 
 def parse_arguments() -> argparse.Namespace:
@@ -97,21 +114,21 @@ def parse_arguments() -> argparse.Namespace:
                         help="output file path")
     parser.add_argument('--mean', required=False, default=300,
                         type=check_positive,
-                        help="Mean fragment length (default: 10)")
+                        help="Mean fragment length (default: 300)")
     parser.add_argument('--std', required=False, default=60,
                         type=check_positive,
                         help="Standard deviation fragment length \
-                            (defafult: 1)")
-    parser.add_argument('-a', '--A_prob', required=False, default=0.22,
+                            (defafult: 60)")
+    parser.add_argument('-a', '--a_prob', required=False, default=0.22,
                         type=check_prob,
                         help="Probability cut happens after nucleotide A")
-    parser.add_argument('-t', '--T_prob', required=False, default=0.25,
+    parser.add_argument('-t', '--t_prob', required=False, default=0.25,
                         type=check_prob,
                         help="Probability cut happens after nucleotide T")
-    parser.add_argument('-g', '--G_prob', required=False, default=0.25,
+    parser.add_argument('-g', '--g_prob', required=False, default=0.25,
                         type=check_prob,
                         help="Probability cut happens after nucleotide G")
-    parser.add_argument('-c', '--C_prob', required=False, default=0.28,
+    parser.add_argument('-c', '--c_prob', required=False, default=0.28,
                         type=check_prob,
                         help="Probability cut happens after nucleotide C")
     parser.add_argument('-s', '--size', required=False, default=10000,