Assignment 1

.replit

@@ -1,8 +1,22 @@
-modules = ["bash", "python-3.11", "python-3.12"]
+
+modules = ["python-3.12", "bash"]
+
 run = "~/workspace/assignments/grade_hw.sh"
 
 [nix]
 channel = "stable-24_05"
 
 [deployment]
 run = ["sh", "-c", "~/workspace/assignments/grade_hw.sh"]
+
+[workflows]
+runButton = "Run"
+
+[[workflows.workflow]]
+name = "Run"
+author = 39028111
+mode = "sequential"
+
+[[workflows.workflow.tasks]]
+task = "shell.exec"
+args = "python main.py"

assignments/01_howdy/howdy.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-03-24
+Purpose: Print greeting
+"""
+
+import argparse
+from enum import Flag
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Print greeting',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('-g', '--greeting', default= 'Howdy', metavar= 'str', help='The greeting')
+
+    parser.add_argument('-n','--name', default= 'Stranger', metavar= 'str', help='Whom to greet')
+
+    parser.add_argument('-e','--excited', help='Print ! if this flag is present', action='store_true')
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    greeting = args.greeting
+    name = args.name
+    excited = args.excited
+
+    if excited:
+        print(f'{greeting}, {name}!')
+    else:
+        print(f'{greeting}, {name}.')
+
+
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/02_divide/divide.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-04-03
+Purpose: Dividing two numbers
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+    parser = argparse.ArgumentParser(
+    description='Divide two numbers',
+    formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('INT', metavar= 'INT', nargs= 2, type=valid_int, help= 'Numbers to divide')
+    return parser
+
+def valid_int(value):
+    try: 
+        ivalue= int(value)
+    except ValueError:
+        raise argparse.ArgumentTypeError(f'invalid int value: {value}') 
+
+    return ivalue
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    parser = get_args()
+    args = parser.parse_args()
+    numerator, denominator = args.INT
+
+    if args.INT[1] == 0:
+        parser.error('Cannot divide by zero, dum-dum!')
+
+    result = numerator // denominator
+    print(f'{numerator} / {denominator} = {result}')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/03_dna/dna.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-04-05
+Purpose: 
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+    parser = argparse.ArgumentParser(description="Tetranucleotide frequency")
+    parser.add_argument("DNA", help="Input DNA sequence")
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    sequence = args.DNA.upper()
+    a_count = sequence.count('A')
+    c_count = sequence.count('C')
+    g_count = sequence.count('G')
+    t_count = sequence.count('T')
+
+    print(f'{a_count} {c_count} {g_count} {t_count}')
+
+
+
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/04_revc/revc.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-04-05
+Purpose: Print the Reverse complement of DNA
+"""
+
+import argparse
+import os
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Print the reverse complement of DNA',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('DNA', help="Input sequence or file")
+
+
+    return parser.parse_args()
+
+def read_sequence(dna_args): 
+   if os.path.isfile(dna_args):
+     with open(dna_args) as file:  
+        return file.read().strip()
+   else: 
+                   return dna_args.strip()
+
+def reverse_complement(sequence):
+  """Return the reverse complement of a DNA sequence"""
+  complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C', 'a': 't', 't': 'a', 'c': 'g', 'g': 'c'}
+  return ''.join(complement.get(base, base) for base in reversed(sequence))
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    sequence = read_sequence(args.DNA)
+    revc = reverse_complement(sequence) 
+    print(revc)
+
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/05_gc/cgc.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-04-05
+Purpose: Compute GC content
+"""
+
+import argparse
+import os
+import sys
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Compute GC content',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument("FILE", nargs="?", help='Input sequence file')
+
+    return parser.parse_args()
+
+def read_fasta(file):
+    sequences = {} 
+    current_id = None 
+    for line in file:
+            line = line.strip()
+            if line.startswith('>'):
+                current_id = line[1:]
+                sequences[current_id] = ''
+            else:
+                sequences[current_id] += line
+    return sequences
+def gc_content(sequence): 
+    gc = sum(1 for base in sequence if base.upper() in "GC") 
+    return (gc / len(sequence)) * 100 if sequence else 0.0
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    if args.FILE:
+        if not os.path.isfile(args.FILE):
+            print('usage: cgc.py [-h] FILE')
+            print(f"cgc.py: error: No such file or directory: '{args.FILE}'")
+            sys.exit(1)
+        with open(args.FILE) as file:
+            sequences = read_fasta(file)
+    else:
+        sequences = read_fasta(sys.stdin)
+    max_id = None 
+    max_gc = 0.0
+
+    for seq_id, sequence in sequences.items(): 
+        gc = gc_content(sequence) 
+        if gc > max_gc:
+            max_gc = gc
+            max_id = seq_id
+    print(f'{max_id} {max_gc:.6f}')
+
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/06_rna/rna.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-04-05
+Purpose: Transcribe DNA into RNA
+"""
+
+import argparse
+import os
+import sys
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Transcribe DNA into RNA')
+    parser.add_argument('files', metavar= 'FILE', nargs='+', help='Input DNA file', type=str)
+    parser.add_argument('-o', '--out_dir', help='Output directory (default: out', metavar='DIR', default='out') 
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    out_dir = args.out_dir
+    files = args.files
+
+    if not os.path.isdir(out_dir): 
+        os.makedirs(out_dir)
+
+    total_sequences = 0
+    for file in files: 
+        try:      
+            basename = os.path.basename(file)
+            out_path = os.path.join(out_dir, basename) 
+            with open(file) as fh_in, open(out_path, 'wt') as fh_out: 
+                for line in fh_in: 
+                    rna = line.strip().replace("T", "U")
+                    fh_out.write(rna + '\n') 
+                    total_sequences += 1
+        except FileNotFoundError: 
+            print(f"usage: {os.path.basename(sys.argv[0])} [-h]", file=sys.stderr) 
+            print(f"No such file or directory: '{file}'", file=sys.stderr) 
+            sys.exit(1)
+
+    num_files = len(files) 
+    seq_str = 'sequence' if total_sequences == 1 else 'sequences' 
+    file_str = 'file' if num_files == 1 else 'files'
+    print(f'Done, wrote {total_sequences} {seq_str} in {num_files} {file_str} to directory "{out_dir}".')
+
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()