Sync Fork

.replit

@@ -5,4 +5,4 @@ run = "~/workspace/assignments/grade_hw.sh"
 channel = "stable-24_05"
 
 [deployment]
-run = ["sh", "-c", "~/workspace/assignments/grade_hw.sh"]
+run = ["sh", "-c", "~/workspace/assignments/grade_hw.sh"]

01_howdy/howdy.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+"""
+Author : Add your Name <Add your email>
+Date   : 2025-02-03
+Purpose: Add Your Purpose
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Add Your Purpose',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('positional',
+                        metavar='str',
+                        help='A positional argument')
+
+    parser.add_argument('-a',
+                        '--arg',
+                        help='A named string argument',
+                        metavar='str',
+                        type=str,
+                        default='')
+
+    parser.add_argument('-i',
+                        '--int',
+                        help='A named integer argument',
+                        metavar='int',
+                        type=int,
+                        default=0)
+
+    parser.add_argument('-f',
+                        '--file',
+                        help='A readable file',
+                        metavar='FILE',
+                        type=argparse.FileType('rt'),
+                        default=None)
+
+    parser.add_argument('-o',
+                        '--on',
+                        help='A boolean flag',
+                        action='store_true')
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    str_arg = args.arg
+    int_arg = args.int
+    file_arg = args.file
+    flag_arg = args.on
+    pos_arg = args.positional
+
+    print(f'str_arg = "{str_arg}"')
+    print(f'int_arg = "{int_arg}"')
+    print('file_arg = "{}"'.format(file_arg.name if file_arg else ''))
+    print(f'flag_arg = "{flag_arg}"')
+    print(f'positional = "{pos_arg}"')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/01_howdy/howdy.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+"""
+Author : Rose Fragala <rosefragala@arizona.edu>
+Date   : 2025-02-03
+Purpose: Print greeting
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Greetings and Howdy',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('-g', '--greeting',
+                           help='The greeting',
+                           metavar='str',
+                           type=str,
+                           default='Howdy')
+
+    parser.add_argument('-n', '--name',
+                           help='Whom to greet',
+                           metavar='str',
+                           type=str,
+                           default='Stranger')
+
+    parser.add_argument('-e', '--excited',
+                           help='Include an exclamation point',
+                           action='store_true')
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    """To generate and print the greetings! (well, hopefully)"""
+
+    args = get_args()
+    greeting = args.greeting
+    name = args.name
+    punctuation = '!' if args.excited else '.'
+    print(f'{greeting}, {name}{punctuation}')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/02_divide/divide.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+"""
+Author : Rose Fragala <rosefragala@arizona.edu>
+Date   : 2025-02-09
+Purpose: To divide two required integer values.
+"""
+
+import argparse
+import sys
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Add Your Purpose',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser = argparse.ArgumentParser(description= 'Divide two numbers')
+    parser.add_argument('INT', type = int, nargs = 2, help = 'Numbers to divide')
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    """Perform Integer Division"""
+
+    args = get_args()
+    num1, num2 = args.INT
+    if num2 == 0:
+        print('usage: divide.py [-h] INT INT', file=sys.stderr)
+        print('Cannot divide by zero, dum-dum!', file=sys.stderr)
+        sys.exit(1)
+
+    result = num1 // num2
+    print(f'{num1} / {num2} = {result}')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/03_dna/dna.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+"""
+Author : Rose Fragala <rosefragala@arizona.edu>
+Date   : 2025-02-13
+Purpose: count tetranucleotide frequency
+"""
+
+import argparse
+
+# --------------------------------------------------
+
+
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Tetranucleotide frequency',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('DNA',
+                        metavar='DNA',
+                        help='Input DNA sequence')
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+
+
+def count_nucleotides(dna):
+    """Count tetranucleotide frequency"""
+    counts = {"A": 0, "C": 0, "G": 0, "T": 0}
+    dna = dna.replace("\n", "").replace("\t", "").replace(" ", "")
+
+    for nucleotide in dna:
+        if nucleotide in counts:
+            counts[nucleotide] += 1
+        else:
+            raise ValueError(
+                f"Invalid character in DNA sequence: {nucleotide}")
+    return counts
+
+
+# --------------------------------------------------
+
+
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    dna = args.DNA.upper().strip()
+    counts = count_nucleotides(dna)
+
+    print(counts["A"], counts["C"], counts["G"], counts["T"])
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/04_revc/revc.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+"""
+Author : Rose Fragala <rosefragala@arizona.edu>
+Date   : 2025-02-19
+Purpose: Print the reverse complement of a DNA sequence
+"""
+
+
+import argparse
+
+
+COMPLEMENTS = str.maketrans("ACGTacgt", "TGCAtgca")
+
+
+# --------------------------------------------------
+
+
+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',
+                        metavar='DNA',
+                        help='Input sequence or file')
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+
+
+def reverse_complement(dna: str) -> str:
+    """Return the reverse complement of a DNA sequence"""
+    return dna[::-1].translate(COMPLEMENTS)
+
+
+# --------------------------------------------------
+
+
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    input_data = args.DNA
+
+    try:
+        with open(input_data, 'rt', encoding='utf-8') as file:
+            dna = file.read().strip()
+    except FileNotFoundError:
+        dna = input_data.strip()
+
+    print(reverse_complement(dna))
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/04_revc/tests/inputs/input1.txt

@@ -0,0 +1 @@
+AAAACCCGGT

assignments/04_revc/tests/inputs/output1.txt

@@ -0,0 +1 @@
+ACCGGGTTTT

assignments/04_revc/tests/inputs/output2.txt

@@ -0,0 +1 @@
+TTTAAACCC

assignments/05_gc/cgc.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+"""
+Author : Rose Fragala <rosefragala@arizona.edu>
+Date   : 2025-02-26
+Purpose: To compute GC content in sequencing reads
+"""
+
+import argparse
+import sys
+
+
+# --------------------------------------------------
+
+
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Compute GC content',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('file',
+                        metavar='FILE',
+                        type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
+                        help='Input sequence file')
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+
+
+def gc_content(dna):
+    """Calculate GC content of a sequence"""
+    gc_count = sum(1 for base in dna if base in 'GC')
+    return (gc_count / len(dna)) * 100 if dna else 0
+
+
+# --------------------------------------------------
+
+
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+    dna = {}
+    seq_id = None
+
+    for line in args.file:
+        line = line.strip()
+        if line.startswith('>'):
+            seq_id = line[1:]
+            dna[seq_id] = ''
+        elif seq_id:
+            dna[seq_id] += line
+
+    max_gc_id = None
+    max_gc_value = -1
+
+    for seq_id, dna in dna.items():
+        gc_val = gc_content(dna)
+        if gc_val > max_gc_value:
+            max_gc_id, max_gc_value = seq_id, gc_val
+    if max_gc_id is not None:
+        print(f'{max_gc_id} {max_gc_value:.6f}')
+    else:
+        print("No valid sequences found.", file=sys.stderr)
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

assignments/05_gc/tests/inputs/1.fa

@@ -0,0 +1,9 @@
+>Rosalind_6404
+CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
+TCCCACTAATAATTCTGAGG
+>Rosalind_5959
+CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
+ATATCCATTTGTCAGCAGACACGC
+>Rosalind_0808
+CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
+TGGGAACCTGCGGGCAGTAGGTGGAAT