cleanup

09_grph/solution1.py

@@ -60,6 +60,8 @@ def main() -> None:
         filemode='w',
         level=logging.DEBUG if args.debug else logging.CRITICAL)
 
+    logging.debug('input file = "%s"', args.file.name)
+
     start, end = defaultdict(list), defaultdict(list)
     for rec in SeqIO.parse(args.file, 'fasta'):
         if kmers := find_kmers(str(rec.seq), args.k):

09_grph/solution2_graph.py

@@ -79,6 +79,8 @@ def main() -> None:
         filemode='w',
         level=logging.DEBUG if args.debug else logging.CRITICAL)
 
+    logging.debug('input file = "%s"', args.file.name)
+
     start, end = defaultdict(list), defaultdict(list)
     for rec in SeqIO.parse(args.file, 'fasta'):
         if kmers := find_kmers(str(rec.seq), args.k):

10_lcsm/solution2_binary_search.py

@@ -74,7 +74,7 @@ def binary_search(f: Callable, low: int, high: int) -> int:
     if hi and lo:
         return high
 
-    if not hi and lo:
+    if lo and not hi:
         return binary_search(f, low, mid)
 
     if hi and not lo:

11_mprt/solution2_manual.py

@@ -103,6 +103,7 @@ def test_find_motif() -> None:
     assert find_motif('ANXTX') == [1]
     assert find_motif('NNTSYS') == [0, 1]
     assert find_motif('XNNTSYS') == [1, 2]
+    assert find_motif('XNNTSYSXNNTSYS') == [1, 2, 8, 9]
 
 
 # --------------------------------------------------

13_revp/common.py

@@ -36,7 +36,6 @@ def test_snd() -> None:
 # --------------------------------------------------
 def find_kmers(seq: str, k: int) -> List[str]:
     """ Find k-mers in string """
-
     n = len(seq) - k + 1
     return [] if n < 1 else [seq[i:i + k] for i in range(n)]
 

13_revp/solution2_operator_eq_if.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+""" Locating Restriction Sites """
+
+import argparse
+import operator
+import sys
+from typing import NamedTuple, TextIO
+from Bio import SeqIO, Seq
+from common import find_kmers
+
+
+class Args(NamedTuple):
+    """ Command-line arguments """
+    file: TextIO
+
+
+# --------------------------------------------------
+def get_args() -> Args:
+    """ Get command-line arguments """
+
+    parser = argparse.ArgumentParser(
+        description='Locating Restriction Sites',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('file',
+                        help='Input FASTA file',
+                        metavar='FILE',
+                        type=argparse.FileType('rt'))
+
+    args = parser.parse_args()
+
+    return Args(args.file)
+
+
+# --------------------------------------------------
+def main() -> None:
+    """ Make a jazz noise here """
+
+    args = get_args()
+    if seqs := [str(rec.seq) for rec in SeqIO.parse(args.file, 'fasta')]:
+        seq = seqs[0]
+
+        for k in range(4, 13):
+            kmers = find_kmers(seq, k)
+            revc = list(map(Seq.reverse_complement, kmers))
+
+            for pos, pair in enumerate(zip(kmers, revc)):
+                if operator.eq(*pair):
+                    print(pos + 1, k)
+    else:
+        sys.exit(f'"{args.file.name}" contains no sequences.')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

13_revp/solution2_operator_eq.py → 13_revp/solution2_operator_eq_lc.py

@@ -40,14 +40,6 @@ def main() -> None:
     if seqs := [str(rec.seq) for rec in SeqIO.parse(args.file, 'fasta')]:
         seq = seqs[0]
 
-        # for k in range(4, 13):
-        #     kmers = find_kmers(seq, k)
-        #     revc = list(map(Seq.reverse_complement, kmers))
-
-        #     for pos, pair in enumerate(zip(kmers, revc)):
-        #         if operator.eq(*pair):
-        #             print(pos + 1, k)
-
         for k in range(4, 13):
             kmers = find_kmers(seq, k)
             revc = map(Seq.reverse_complement, kmers)