From 246bed5bc9ce517c78f83a33f04275d45cd63900 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 22 Jan 2025 01:03:38 +0000
Subject: [PATCH 01/22] testing commit

---
 .replit    |  8 ++++++
 bin/new.py |  2 ++
 testing.py | 72 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 82 insertions(+)
 create mode 100644 .replit
 create mode 100755 testing.py

diff --git a/.replit b/.replit
new file mode 100644
index 0000000..688516d
--- /dev/null
+++ b/.replit
@@ -0,0 +1,8 @@
+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"]
diff --git a/bin/new.py b/bin/new.py
index 8a2cf7b..be10290 100755
--- a/bin/new.py
+++ b/bin/new.py
@@ -192,3 +192,5 @@ def get_defaults():
 # --------------------------------------------------
 if __name__ == '__main__':
     main()
+
+
diff --git a/testing.py b/testing.py
new file mode 100755
index 0000000..34c95cf
--- /dev/null
+++ b/testing.py
@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+"""
+Author : Add your Name <Add your email>
+Date   : 2025-01-22
+Purpose: This is a test script
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='This is a test script',
+        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()

From 60f627d615e105aae9dbe36f087e86eb658bb965 Mon Sep 17 00:00:00 2001
From: Bonnie Hurwitz <bhurwitz@arizona.edu>
Date: Sun, 23 Mar 2025 20:20:28 -0400
Subject: [PATCH 02/22] fixing test.py in 07_syndna

---
 assignments/07_syndna/test.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/assignments/07_syndna/test.py b/assignments/07_syndna/test.py
index 4e08726..0f8f5a3 100644
--- a/assignments/07_syndna/test.py
+++ b/assignments/07_syndna/test.py
@@ -7,12 +7,16 @@
 import string
 from subprocess import getstatusoutput
 from Bio import SeqIO
-from Bio.SeqUtils import GC
+#from Bio.SeqUtils import GC
+from Bio.SeqUtils import gc_fraction
 from numpy import mean
 from itertools import chain
 
 prg = './syndna.py'
 
+# --------------------------------------------------
+def GC(sequence):
+    return 100 * gc_fraction(sequence, ambiguous="ignore")
 
 # --------------------------------------------------
 def random_string():

From 3810cdfdbde3f11d351bec54412a0f58df5df197 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Mon, 24 Mar 2025 02:58:21 +0000
Subject: [PATCH 03/22] Assignment 1 commit and exercise 1

---
 assignments/01_howdy/howdy.py | 46 +++++++++++++++++++++++++++++++++++
 exercises/01_hello/hello.py   | 20 +++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100755 assignments/01_howdy/howdy.py
 create mode 100755 exercises/01_hello/hello.py

diff --git a/assignments/01_howdy/howdy.py b/assignments/01_howdy/howdy.py
new file mode 100755
index 0000000..8189145
--- /dev/null
+++ b/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()
\ No newline at end of file
diff --git a/exercises/01_hello/hello.py b/exercises/01_hello/hello.py
new file mode 100755
index 0000000..364af48
--- /dev/null
+++ b/exercises/01_hello/hello.py
@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# Purpose: Say Hello
+import argparse
+
+
+def get_args():
+  parser = argparse.ArgumentParser(description='Say hello')
+  parser.add_argument('-n', '--name', metavar='name', 
+                      default='World', help='Name to greet')
+
+  return parser.parse_args()
+
+
+def main():
+    args = get_args()
+print('Hello, ' + args.name + '!') 
+
+if __name__ == '__main__':
+    main()
+

From 9825362d1edcd589b098b31130389404208a713c Mon Sep 17 00:00:00 2001
From: kukichk0 <39028111-kukichk0@users.noreply.replit.com>
Date: Sat, 5 Apr 2025 03:39:17 +0000
Subject: [PATCH 04/22] Checkpoint before assistant change: Fix division by
 zero error by adding error handling.

Replit-Commit-Author: Assistant
---
 assignments/02_divide/divide.py     | 42 +++++++++++++++++++++++++++++
 exercises/02_crowsnest/crowsnest.py | 40 +++++++++++++++++++++++++++
 exercises/03_picnic/picnic.py       | 36 +++++++++++++++++++++++++
 3 files changed, 118 insertions(+)
 create mode 100755 assignments/02_divide/divide.py
 create mode 100755 exercises/02_crowsnest/crowsnest.py
 create mode 100755 exercises/03_picnic/picnic.py

diff --git a/assignments/02_divide/divide.py b/assignments/02_divide/divide.py
new file mode 100755
index 0000000..e0bca5e
--- /dev/null
+++ b/assignments/02_divide/divide.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-04-03
+Purpose: Add Your Purpose
+"""
+
+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
+    result = numerator // denominator
+    print(f'{numerator} / {denominator} = {result}')
+    if args.INT[1] == 0:
+            parser.error('Cannot divide by zero, dum-dum!')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/exercises/02_crowsnest/crowsnest.py b/exercises/02_crowsnest/crowsnest.py
new file mode 100755
index 0000000..fa30671
--- /dev/null
+++ b/exercises/02_crowsnest/crowsnest.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+"""
+Author : Add your Name <Add your email>
+Date   : 2025-04-01
+Purpose: Crow's Nest -- choose the correct article
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Crows Nest -- choose the correct article',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('word', 
+                        metavar='word',
+                        help= 'A word')
+
+    
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+                    args = get_args()
+                    word = args.word
+                    
+
+
+                    if word[0].lower()      in 'aeiou':                                    article = 'an' 
+                    else: article = 'a'
+                    print(f'Ahoy, Captain, {article} {word} off the larboard bow!')
+# -----------------------------------------------
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/exercises/03_picnic/picnic.py b/exercises/03_picnic/picnic.py
new file mode 100755
index 0000000..b6890f8
--- /dev/null
+++ b/exercises/03_picnic/picnic.py
@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+"""
+Author : Add your Name <Add your email>
+Date   : 2025-04-03
+Purpose: Add Your Purpose
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Picnic game',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('Item', metavar= 'str', nargs='+', help='Item(s) to bring')
+    parser.add_argument('-s', '--sorted', action='store_true', help='Sort the items')
+
+   
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    args = get_args()
+    items = args.Item
+    print(f'You are bringing {items}.')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

From e520d382280da57ccdcba788b373f16782d1c9ef Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Sat, 5 Apr 2025 03:39:44 +0000
Subject: [PATCH 05/22] Assistant checkpoint: Move zero division check before
 division operation

Assistant generated file changes:
- assignments/02_divide/divide.py: Fix zero division error check

---

User prompt:

how do I fix this ./divide.py 1 0
Traceback (most recent call last):
  File "/home/runner/workspace/assignments/02_divide/./divide.py", line 42, in <module>
    main()
  File "/home/runner/workspace/assignments/02_divide/./divide.py", line 34, in main
    result = numerator // denominator
             ~~~~~~~~~~^^~~~~~~~~~~~~
ZeroDivisionError: integer division or modulo by zero

Replit-Commit-Author: Assistant
Replit-Commit-Session-Id: f998859b-af06-4f4a-bca1-0716a747d838
---
 assignments/02_divide/divide.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/assignments/02_divide/divide.py b/assignments/02_divide/divide.py
index e0bca5e..d091e28 100755
--- a/assignments/02_divide/divide.py
+++ b/assignments/02_divide/divide.py
@@ -22,7 +22,7 @@ def valid_int(value):
         ivalue= int(value)
     except ValueError:
         raise argparse.ArgumentTypeError(f'invalid int value: {value}') 
-    
+
     return ivalue
 # --------------------------------------------------
 def main():
@@ -31,10 +31,12 @@ def main():
     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 args.INT[1] == 0:
-            parser.error('Cannot divide by zero, dum-dum!')
 
 
 # --------------------------------------------------

From b366bb002332a5432ab207bf4b2c7333f553b39f Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Sat, 5 Apr 2025 03:45:06 +0000
Subject: [PATCH 06/22] Submitting Homework 2

---
 assignments/02_divide/divide.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assignments/02_divide/divide.py b/assignments/02_divide/divide.py
index d091e28..8f039e7 100755
--- a/assignments/02_divide/divide.py
+++ b/assignments/02_divide/divide.py
@@ -2,7 +2,7 @@
 """
 Author : Khaira Kukich <kukichk0@arizona.edu>
 Date   : 2025-04-03
-Purpose: Add Your Purpose
+Purpose: Dividing two numbers
 """
 
 import argparse

From 667000f1febe46efbc06ea6add2490f573dc8f4b Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Sat, 5 Apr 2025 04:00:57 +0000
Subject: [PATCH 07/22] Fixing Shell Error

---
 .replit | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.replit b/.replit
index 9238a6e..5da2814 100644
--- a/.replit
+++ b/.replit
@@ -1,7 +1,6 @@
 
 modules = ["python-3.12", "bash"]
-=======
-modules = ["bash", "python-3.11", "python-3.12"]
+
 run = "~/workspace/assignments/grade_hw.sh"
 
 [nix]

From c2fa805016901784b282e39b5637e6fec1687ce0 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Sat, 5 Apr 2025 04:02:04 +0000
Subject: [PATCH 08/22] Assistant checkpoint: Configure workflow to run Python

Assistant generated file changes:
- main.py: Create basic Python file
- .replit: Updated app configuration

---

User prompt:

it didnt fix my shell

Replit-Commit-Author: Assistant
Replit-Commit-Session-Id: 6604206e-2416-4800-9679-4d1cd1e56756
---
 .replit | 12 ++++++++++++
 main.py |  6 ++++++
 2 files changed, 18 insertions(+)
 create mode 100644 main.py

diff --git a/.replit b/.replit
index 5da2814..8c115c8 100644
--- a/.replit
+++ b/.replit
@@ -8,3 +8,15 @@ 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"
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..32090c4
--- /dev/null
+++ b/main.py
@@ -0,0 +1,6 @@
+
+def main():
+    print("Hello from Python!")
+
+if __name__ == "__main__":
+    main()

From 4d4d687c0739abeec1d3d741a011b9607d9a30b8 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Sat, 5 Apr 2025 04:18:53 +0000
Subject: [PATCH 09/22] Submitting Homework 3

---
 assignments/03_dna/dna.py | 38 ++++++++++++++++++++++++++++++++++++++
 bin/new.py                |  2 +-
 2 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100755 assignments/03_dna/dna.py

diff --git a/assignments/03_dna/dna.py b/assignments/03_dna/dna.py
new file mode 100755
index 0000000..f2ce0b8
--- /dev/null
+++ b/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()
diff --git a/bin/new.py b/bin/new.py
index bccd0e1..a696220 100755
--- a/bin/new.py
+++ b/bin/new.py
@@ -191,4 +191,4 @@ def get_defaults():
 
 # --------------------------------------------------
 if __name__ == '__main__':
-main() 
+    main() 

From bd3b8b0e3e2959e5f213eb845dec82daca558f0e Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Sat, 5 Apr 2025 04:54:19 +0000
Subject: [PATCH 10/22] Submitting Homework 4

---
 assignments/04_revc/revc.py | 48 +++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100755 assignments/04_revc/revc.py

diff --git a/assignments/04_revc/revc.py b/assignments/04_revc/revc.py
new file mode 100755
index 0000000..aabf6f8
--- /dev/null
+++ b/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()

From 7b1e033683c46a731b3f95f9d8776d2589d129a5 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Sun, 6 Apr 2025 03:40:53 +0000
Subject: [PATCH 11/22] Assignment 5

---
 assignments/05_gc/Rosalind_0808 |  0
 assignments/05_gc/Rosalind_5959 |  0
 assignments/05_gc/Rosalind_6404 |  0
 assignments/05_gc/cgc.py        | 65 +++++++++++++++++++++++++++++++++
 4 files changed, 65 insertions(+)
 create mode 100644 assignments/05_gc/Rosalind_0808
 create mode 100644 assignments/05_gc/Rosalind_5959
 create mode 100644 assignments/05_gc/Rosalind_6404
 create mode 100755 assignments/05_gc/cgc.py

diff --git a/assignments/05_gc/Rosalind_0808 b/assignments/05_gc/Rosalind_0808
new file mode 100644
index 0000000..e69de29
diff --git a/assignments/05_gc/Rosalind_5959 b/assignments/05_gc/Rosalind_5959
new file mode 100644
index 0000000..e69de29
diff --git a/assignments/05_gc/Rosalind_6404 b/assignments/05_gc/Rosalind_6404
new file mode 100644
index 0000000..e69de29
diff --git a/assignments/05_gc/cgc.py b/assignments/05_gc/cgc.py
new file mode 100755
index 0000000..dffa25b
--- /dev/null
+++ b/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()

From 58026a1c762877256cecad2176ec2b6e19227c38 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Tue, 6 May 2025 19:52:44 +0000
Subject: [PATCH 12/22] Submitting Assignment 6

---
 assignments/06_rna/rna.py | 58 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100755 assignments/06_rna/rna.py

diff --git a/assignments/06_rna/rna.py b/assignments/06_rna/rna.py
new file mode 100755
index 0000000..1a8decb
--- /dev/null
+++ b/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()

From fc98ec3d85a0791459105fd3600bc0a270cc4518 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Tue, 6 May 2025 20:43:19 +0000
Subject: [PATCH 13/22] Submitting Assignment 7

---
 assignments/07_syndna/syndna.py | 117 ++++++++++++++++++++++++++++++++
 1 file changed, 117 insertions(+)
 create mode 100755 assignments/07_syndna/syndna.py

diff --git a/assignments/07_syndna/syndna.py b/assignments/07_syndna/syndna.py
new file mode 100755
index 0000000..5f74adb
--- /dev/null
+++ b/assignments/07_syndna/syndna.py
@@ -0,0 +1,117 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-04-26
+Purpose: Create synthetic DNA/RNA sequences
+"""
+
+import argparse
+import random
+import sys
+
+
+def get_args():
+    """Get command-line arguments"""
+    parser = argparse.ArgumentParser(
+        description='Create synthetic sequences',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('-o',
+                        '--outfile',
+                        type=argparse.FileType('wt'),
+                        default='out.fa',
+                        help='Output filename')
+
+    parser.add_argument('-t',
+                        '--seqtype',
+                        metavar='str',
+                        type=str.lower,
+                        choices=['dna', 'rna'],
+                        default='dna',
+                        help='DNA or RNA')
+
+    parser.add_argument('-n',
+                        '--numseqs',
+                        metavar='int',
+                        type=int,
+                        default=10,
+                        help='Number of sequences to create')
+
+    parser.add_argument('-m',
+                        '--minlen',
+                        metavar='int',
+                        type=int,
+                        default=50,
+                        help='Minimum length')
+
+    parser.add_argument('-x',
+                        '--maxlen',
+                        metavar='int',
+                        type=int,
+                        default=75,
+                        help='Maximum length')
+
+    parser.add_argument('-p',
+                        '--pctgc',
+                        metavar='float',
+                        type=float,
+                        default=0.5,
+                        help='Percent GC')
+
+    parser.add_argument('-s',
+                        '--seed',
+                        metavar='int',
+                        type=int,
+                        default=None,
+                        help='Random seed')
+
+    args = parser.parse_args()
+
+    
+    if not 0 < args.pctgc < 1:
+        parser.error(f'--pctgc "{args.pctgc}" must be between 0 and 1')
+
+    
+    if args.minlen < 1:
+        parser.error('--minlen must be > 0')
+    if args.maxlen < args.minlen:
+        parser.error('--maxlen must be >= --minlen')
+
+    return args
+
+
+def create_pool(pctgc, max_len, seq_type):
+    """Create the pool of bases"""
+    t_or_u = 'T' if seq_type == 'dna' else 'U'
+    num_gc = int((pctgc / 2) * max_len)
+    num_at = int(((1 - pctgc) / 2) * max_len)
+    pool = 'A' * num_at + 'C' * num_gc + 'G' * num_gc + t_or_u * num_at
+
+    
+    for _ in range(max_len - len(pool)):
+        pool += random.choice(pool)
+
+    return ''.join(sorted(pool))
+
+
+def main():
+    """Main program"""
+    args = get_args()
+    random.seed(args.seed)
+    pool = create_pool(args.pctgc, args.maxlen, args.seqtype)
+
+    for i in range(1, args.numseqs + 1):
+        seq_len = random.randint(args.minlen, args.maxlen)
+        seq = ''.join(random.sample(pool, seq_len))
+        args.outfile.write(f'>{i}\n{seq}\n')
+
+    args.outfile.close()
+
+    
+    plural_seq = 'sequence' if args.numseqs == 1 else 'sequences'
+    print(f'Done, wrote {args.numseqs} {args.seqtype.upper()} {plural_seq} to "{args.outfile.name}".')
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

From d7e8222082d99c009d4ea3439083d2bb0785ceb1 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 7 May 2025 04:29:11 +0000
Subject: [PATCH 14/22] Submitting Assignment 8

---
 assignments/08_common/common.py | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100755 assignments/08_common/common.py

diff --git a/assignments/08_common/common.py b/assignments/08_common/common.py
new file mode 100755
index 0000000..f532df0
--- /dev/null
+++ b/assignments/08_common/common.py
@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-05-06
+Purpose: Find common words between two files
+"""
+
+import argparse
+import sys
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Find common words',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('file1',
+                        metavar='FILE1', type=argparse.FileType('rt'),
+                        help='Input file 1')
+
+    parser.add_argument('file2',
+                        help='Input file 2',
+                        metavar='FILE2',
+                        type=argparse.FileType('rt'))
+
+    parser.add_argument('-o',
+                        '--outfile',
+                        help='Output file (default: stdout)',
+                        metavar='FILE',
+                        type=argparse.FileType('wt'),
+                        default=sys.stdout)
+
+    return parser.parse_args()
+def get_words(filehandle): 
+                    words = set()
+                    for line in filehandle:
+                        for word in line.split():
+                            words.add(word)
+                    return words 
+
+# --------------------------------------------------
+def main():
+    """Make a jazz noise here"""
+
+    args = get_args()
+
+    words1 = get_words(args.file1) 
+    words2 = get_words(args.file2)
+
+    common = sorted(words1 & words2)
+
+    for word in common:
+                        print(word, file=args.outfile)
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

From a0b0e9b97da6a13301c349abb6e30268f0c1896b Mon Sep 17 00:00:00 2001
From: kukichk0 <39028111-kukichk0@users.noreply.replit.com>
Date: Wed, 7 May 2025 14:51:57 +0000
Subject: [PATCH 15/22] Checkpoint before assistant change: Add tools to
 analyze data, filter records, and annotate BLAST results

Implements blastomatic.py for BLAST annotation and csvfilter.py for filtering CSV files based on user input.

Replit-Commit-Author: Assistant
---
 assignments/09_blastomatic/blastomatic.py | 106 ++++++++++++++++++++++
 extra_practice/09_csvfilter/csvfilter.py  |  46 ++++++++++
 2 files changed, 152 insertions(+)
 create mode 100755 assignments/09_blastomatic/blastomatic.py
 create mode 100755 extra_practice/09_csvfilter/csvfilter.py

diff --git a/assignments/09_blastomatic/blastomatic.py b/assignments/09_blastomatic/blastomatic.py
new file mode 100755
index 0000000..80c558d
--- /dev/null
+++ b/assignments/09_blastomatic/blastomatic.py
@@ -0,0 +1,106 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-05-07
+Purpose: Annotate BLAST output
+"""
+
+import argparse
+import csv 
+import sys
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+    parser = argparse.ArgumentParser(
+                            description='Annotate BLAST output',
+                            formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('-b', '--blasthits',
+                        metavar='str', type=argparse.FileType('rt'), required=True,
+                        help='BLAST -outfmt 6')
+
+    parser.add_argument('-a', '--annotations', metavar='str',
+                        help='Annotations file',
+                        type=argparse.FileType('rt'),
+                        required=True)
+
+    parser.add_argument('-o', '--outfile',
+                        help='Output file',
+                        type=argparse.FileType('wt'),
+                        default='out.csv', metavar='str')
+
+    parser.add_argument('-d', '--delimiter',
+                        help='Output field delimiter',
+                        default=',',
+                        metavar='str')
+
+    parser.add_argument('-p', '--pctid',
+                        help='Minimum percent identity',
+                        type=float, metavar='float',
+                        default=0.0)
+    return parser.parse_args() 
+
+
+# --------------------------------------------------
+def guess_delimiter(filename):
+    with open(filename, 'rt', newline='') as f:
+        sample = f.read(1024)
+        sniffer = csv.Sniffer()
+        return sniffer.sniff(sample).delimiter
+
+
+# --------------------------------------------------
+def main():
+    args = get_args()
+
+    try:
+        ann_delim = guess_delimiter(args.annotations.name)
+        print(f'Guessed delimiter for annotations file: {ann_delim}')
+        reader = csv.DictReader(args.annotations, delimiter=ann_delim)
+
+        annotations = {}
+        for row in reader:
+            qseqid = row.get('qseqid')
+            if qseqid:
+                annotations[qseqid] = row
+        print(f'Annotations (first 3 rows): {list(annotations.items())[:3]}')
+        out_fields = ['qseqid', 'pident', 'depth', 'lat_lon']
+        writer = csv.DictWriter(args.outfile, fieldnames=out_fields, delimiter=args.delimiter)
+        writer.writeheader()
+
+        reader = csv.reader(args.blasthits, delimiter='\t')
+        count = 0
+        for row in reader:
+            if len(row) < 3:
+                continue
+
+            qseqid = row[0]
+            try:
+                pident = float(row[2])
+            except ValueError:
+                continue
+            print(f'Processing BLAST hit: {qseqid}, pident: {pident}')
+            if qseqid not in annotations: 
+                print(f'DEBUG: {qseqid} not found in annotations')
+            elif pident >= args.pctid: 
+                ann = annotations[qseqid]
+                writer.writerow({
+                    'qseqid': qseqid,
+                    'pident': f'{pident:.3f}',
+                    'depth': ann.get('depth', ''),
+                    'lat_lon': ann.get('lat_lon', '')
+                })
+                count += 1
+
+        print(f'Exported {count} hits to "{args.outfile.name}".')
+
+    except Exception as e:
+        print(f'Error: {e}', file=sys.stderr)
+        sys.exit(1)
+
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/extra_practice/09_csvfilter/csvfilter.py b/extra_practice/09_csvfilter/csvfilter.py
new file mode 100755
index 0000000..9952280
--- /dev/null
+++ b/extra_practice/09_csvfilter/csvfilter.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+"""
+Author : Add your Name <Add your email>
+Date   : 2025-05-07
+Purpose: Add Your Purpose
+"""
+
+import argparse
+import csv
+import re
+import sys
+def get_args():
+    """Get command-line arguments"""
+    parser = argparse.ArgumentParser(description='Filter delimited records')
+    parser.add_argument('-f', '--file', type=argparse.FileType('r'), required=True, help='Input file')
+    parser.add_argument('-v', '--val', required=True, help='Value for filter')
+    parser.add_argument('-c', '--col', help='Column name for filter')
+    parser.add_argument('-o', '--outfile', type=str, default='out.csv', help='Output file name')
+    parser.add_argument('-d', '--delimiter', default=',', help='Input file delimiter (default: ",")')
+    return parser.parse_args()
+def main():
+    args = get_args()
+   
+    reader = csv.DictReader(args.file, delimiter=args.delimiter)
+    fieldnames = reader.fieldnames
+   
+    if args.col and args.col not in fieldnames:
+      print(f'Error: "{args.col}" is not a valid column! Choose from {", ".joinfieldnames}', file=sys.stderr)
+      sys.exit(1)
+   
+    writer = csv.DictWriter(open(args.outfile, 'w', newline=''), fieldnames=fieldnames, delimiter=args.delimiter)
+    writer.writeheader()
+    
+    count = 0
+   
+    for row in reader:
+        if args.col:  
+            text = row[args.col]
+        else:  
+            text = " ".join(row.values())
+        if re.search(args.val, text, re.IGNORECASE):
+            writer.writerow(row)
+            count += 1
+    print(f'Done, wrote {count} to "{args.outfile}".')
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 428e64041df00279fb4d1784d23ccc1a603709ea Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 7 May 2025 14:52:10 +0000
Subject: [PATCH 16/22] Assistant checkpoint: Fix string join syntax in error
 message

Assistant generated file changes:
- extra_practice/09_csvfilter/csvfilter.py: Fix string formatting for fieldnames

---

User prompt:

how do i fix it

Replit-Commit-Author: Assistant
Replit-Commit-Session-Id: 86e886b0-77b0-4e21-801d-9f59a68a39ac
---
 extra_practice/09_csvfilter/csvfilter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/extra_practice/09_csvfilter/csvfilter.py b/extra_practice/09_csvfilter/csvfilter.py
index 9952280..ecbc0bf 100755
--- a/extra_practice/09_csvfilter/csvfilter.py
+++ b/extra_practice/09_csvfilter/csvfilter.py
@@ -25,7 +25,7 @@ def main():
     fieldnames = reader.fieldnames
    
     if args.col and args.col not in fieldnames:
-      print(f'Error: "{args.col}" is not a valid column! Choose from {", ".joinfieldnames}', file=sys.stderr)
+      print(f'Error: "{args.col}" is not a valid column! Choose from {", ".join(fieldnames)}', file=sys.stderr)
       sys.exit(1)
    
     writer = csv.DictWriter(open(args.outfile, 'w', newline=''), fieldnames=fieldnames, delimiter=args.delimiter)

From a7f73ae095ca28e05aa1394730db665ae7d90182 Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 7 May 2025 14:57:23 +0000
Subject: [PATCH 17/22] submitting assignment 9 csvfilter.py

---
 extra_practice/09_csvfilter/csvfilter.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/extra_practice/09_csvfilter/csvfilter.py b/extra_practice/09_csvfilter/csvfilter.py
index ecbc0bf..cf1a226 100755
--- a/extra_practice/09_csvfilter/csvfilter.py
+++ b/extra_practice/09_csvfilter/csvfilter.py
@@ -18,6 +18,7 @@ def get_args():
     parser.add_argument('-o', '--outfile', type=str, default='out.csv', help='Output file name')
     parser.add_argument('-d', '--delimiter', default=',', help='Input file delimiter (default: ",")')
     return parser.parse_args()
+                    
 def main():
     args = get_args()
    
@@ -25,10 +26,10 @@ def main():
     fieldnames = reader.fieldnames
    
     if args.col and args.col not in fieldnames:
-      print(f'Error: "{args.col}" is not a valid column! Choose from {", ".join(fieldnames)}', file=sys.stderr)
-      sys.exit(1)
-   
-    writer = csv.DictWriter(open(args.outfile, 'w', newline=''), fieldnames=fieldnames, delimiter=args.delimiter)
+       print(f'Error: --col "{args.col}" not a valid column!', file=sys.stderr)
+       sys.exit(1)
+    else: 
+     writer = csv.DictWriter(open(args.outfile, 'w', newline=''), fieldnames=fieldnames, delimiter=args.delimiter)
     writer.writeheader()
     
     count = 0

From 51ef593b7e37bcef67895ef72fd3b6ecc5afb57e Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 7 May 2025 15:05:27 +0000
Subject: [PATCH 18/22] Submitting assignment 10 !!

---
 assignments/10_conserved/conserved.py | 63 +++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100755 assignments/10_conserved/conserved.py

diff --git a/assignments/10_conserved/conserved.py b/assignments/10_conserved/conserved.py
new file mode 100755
index 0000000..ef8eeb0
--- /dev/null
+++ b/assignments/10_conserved/conserved.py
@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-05-07
+Purpose: Find Conserved Bases
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(description='Find conserved bases')
+    parser.add_argument('file', metavar='FILE', type=argparse.FileType('r'),
+                        help='Input file with sequences')
+    return parser.parse_args()
+
+def read_sequences(file):
+    """Read sequences from the file and return them as a list"""
+    sequences = []
+    for line in file:
+        line = line.strip()
+        if not line.startswith('>'):  
+            sequences.append(line)
+    return sequences
+
+def find_conserved_bases(sequences):
+    """Find conserved bases in the sequences"""
+    
+    if len(set(len(seq) for seq in sequences)) > 1:
+        raise ValueError("Sequences have different lengths")
+
+    conserved = []
+    for i in range(len(sequences[0])):  
+        bases = [seq[i] for seq in sequences]
+        if len(set(bases)) == 1:  
+            conserved.append('|')
+        else:
+            conserved.append('X')
+    return ''.join(conserved)
+
+def main():
+    args = get_args()
+
+    try:
+        
+        sequences = read_sequences(args.file)
+
+        
+        for seq in sequences:
+            print(seq)
+
+       
+        conserved_bases = find_conserved_bases(sequences)
+        print(conserved_bases)
+
+    except Exception as e:
+        print(f"Error: {e}")
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 50fb6021e69ca8aeb8f525fc7513a9df173a5347 Mon Sep 17 00:00:00 2001
From: kukichk0 <39028111-kukichk0@users.noreply.replit.com>
Date: Wed, 7 May 2025 15:48:07 +0000
Subject: [PATCH 19/22] Checkpoint before assistant change: Add programs to
 process DNA sequences by encoding and summarizing files

Implements run-length encoding in `run.py` and FASTA file summarization in `seqmagique.py` using `argparse` and `tabulate`.

Replit-Commit-Author: Assistant
---
 assignments/11_run_length/run.py        |  67 ++++++++++++++++
 assignments/12_seqmagique/seqmagique.py | 102 ++++++++++++++++++++++++
 2 files changed, 169 insertions(+)
 create mode 100755 assignments/11_run_length/run.py
 create mode 100755 assignments/12_seqmagique/seqmagique.py

diff --git a/assignments/11_run_length/run.py b/assignments/11_run_length/run.py
new file mode 100755
index 0000000..91ba183
--- /dev/null
+++ b/assignments/11_run_length/run.py
@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-05-07
+Purpose: Run Length Encoding
+"""
+
+import argparse
+import os
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Run-length encoding/data compression')
+    parser.add_argument('text',
+                        metavar='str',
+                        help='DNA text or file')
+    return parser.parse_args()
+
+
+def rle(seq):
+    """Return run-length encoded string"""
+    if not seq:
+        return ''
+
+    result = []
+    count = 1
+    prev = seq[0]
+
+    for base in seq[1:]:
+        if base == prev:
+            count += 1
+        else:
+            result.append(prev + (str(count) if count > 1 else ''))
+            prev = base
+            count = 1
+    result.append(prev + (str(count) if count > 1 else ''))
+    return ''.join(result)
+
+
+def main():
+    args = get_args()
+
+    if os.path.isfile(args.text):
+        with open(args.text) as fh:
+            for line in fh:
+                line = line.strip()
+                if line:
+                    print(rle(line))
+    else:
+        print(rle(args.text))
+
+
+def test_rle():
+    """Test rle"""
+    assert rle('') == ''
+    assert rle('A') == 'A'
+    assert rle('ACGT') == 'ACGT'
+    assert rle('AA') == 'A2'
+    assert rle('AAAAA') == 'A5'
+    assert rle('ACCGGGTTTT') == 'AC2G3T4'
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/assignments/12_seqmagique/seqmagique.py b/assignments/12_seqmagique/seqmagique.py
new file mode 100755
index 0000000..64ba6b6
--- /dev/null
+++ b/assignments/12_seqmagique/seqmagique.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-05-07
+Purpose: Summarize FASTA file
+"""
+
+import argparse
+import os 
+import sys
+from tabulate import tabulate 
+from typing import List 
+
+
+# --------------------------------------------------
+def get_args():
+    """Parse command-line arguments"""
+    parser = argparse.ArgumentParser(
+        description="Argparse Python script",
+    )
+    parser.add_argument(
+        "files",
+        metavar="FILE",
+        type=str,
+        nargs="+",
+        help="Input FASTA file(s)",
+    )
+    parser.add_argument(
+        "-t",
+        "--tablefmt",
+        metavar="table",
+        type=str,
+        default="plain",
+        help="Tabulate table style (default: plain)",
+    )
+    return parser.parse_args()
+
+
+def die(msg: str) -> None:
+    """Print error message and exit"""
+    print(f"usage: {sys.argv[0]} [-h] [-t table] FILE [FILE ...]", file=sys.stderr)
+    print(msg, file=sys.stderr)
+    sys.exit(1)
+
+
+def parse_fasta(filename: str) -> List[str]:
+    """Parse FASTA file and return list of sequences"""
+    if not os.path.isfile(filename):
+        die(f"No such file or directory: \'{filename}\'")
+
+    sequences = []
+    seq = []
+
+    with open(filename, "rt") as file:
+        for line in file:
+            line = line.strip()
+            if not line:
+                continue
+            if line.startswith(">"):
+                if seq:
+                    sequences.append("".join(seq))
+                    seq = []
+            else:
+                seq.append(line)
+
+        if seq:
+            sequences.append("".join(seq))
+
+    return sequences
+
+
+def main():
+    """Main function"""
+    args = get_args()
+    headers = ["name", "min_len", "max_len", "avg_len", "num_seqs"]
+    rows = []
+
+    for file in args.files:
+        try:
+            seqs = parse_fasta(file)
+            lengths = list(map(len, seqs))
+            num_seqs = len(seqs)
+            min_len = min(lengths) if lengths else 0
+            max_len = max(lengths) if lengths else 0
+            avg_len = sum(lengths) / num_seqs if num_seqs else 0.00
+
+            rows.append([
+                file,
+                min_len,
+                max_len,
+                f"{avg_len:.2f}", 
+                num_seqs,
+            ])
+        except SystemExit:
+            sys.exit(1)
+
+   
+    print(tabulate(rows, headers=headers, tablefmt="plain", numalign="right", stralign="left"))
+
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file

From c0e6f5a3f64e04aedf5e4a1055ce1a79ed50887a Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 7 May 2025 16:29:42 +0000
Subject: [PATCH 20/22] Assignment 12

---
 assignments/12_seqmagique/assert        |  0
 assignments/12_seqmagique/seqmagique.py | 28 +++++++++++++------------
 2 files changed, 15 insertions(+), 13 deletions(-)
 create mode 100644 assignments/12_seqmagique/assert

diff --git a/assignments/12_seqmagique/assert b/assignments/12_seqmagique/assert
new file mode 100644
index 0000000..e69de29
diff --git a/assignments/12_seqmagique/seqmagique.py b/assignments/12_seqmagique/seqmagique.py
index 64ba6b6..191db5d 100755
--- a/assignments/12_seqmagique/seqmagique.py
+++ b/assignments/12_seqmagique/seqmagique.py
@@ -11,7 +11,7 @@
 from tabulate import tabulate 
 from typing import List 
 
-
+#This one is a doozy, yikes, I'll take the 50%
 # --------------------------------------------------
 def get_args():
     """Parse command-line arguments"""
@@ -73,7 +73,7 @@ def main():
     """Main function"""
     args = get_args()
     headers = ["name", "min_len", "max_len", "avg_len", "num_seqs"]
-    rows = []
+    rows = []  
 
     for file in args.files:
         try:
@@ -82,20 +82,22 @@ def main():
             num_seqs = len(seqs)
             min_len = min(lengths) if lengths else 0
             max_len = max(lengths) if lengths else 0
-            avg_len = sum(lengths) / num_seqs if num_seqs else 0.00
-
-            rows.append([
-                file,
-                min_len,
-                max_len,
-                f"{avg_len:.2f}", 
-                num_seqs,
-            ])
+            avg_len = sum(lengths) / num_seqs if num_seqs else 0
+
+            avg_len = str(int(avg_len)) if avg_len == 0 else f"{avg_len:.2f}"
+            rows.append([file, min_len, max_len, avg_len, num_seqs])
         except SystemExit:
             sys.exit(1)
 
-   
-    print(tabulate(rows, headers=headers, tablefmt="plain", numalign="right", stralign="left"))
+    if not rows:  
+        sys.exit(1)  
+
+    print(f"{'name':<26} {'min_len':<8} {'max_len':<8} {'avg_len':<8} {'num_seqs':<8}")
+    for row in rows:
+        name, min_len, max_len, avg_len, num_seqs = row
+        avg_len = f"{avg_len:.2f}" if avg_len != 0 else '0'  
+        num_seqs = str(num_seqs) 
+        print(f"{name:<26} {min_len:<8} {max_len:<8} {avg_len:<8} {num_seqs:<8}")
 
 
 if __name__ == "__main__":

From 5e3f3fdb67f99ee13304b39129fd0a7f45f545af Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 7 May 2025 16:30:40 +0000
Subject: [PATCH 21/22] submitting assignment 11

---
 assignments/11_run_length/run.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/assignments/11_run_length/run.py b/assignments/11_run_length/run.py
index 91ba183..4a152d7 100755
--- a/assignments/11_run_length/run.py
+++ b/assignments/11_run_length/run.py
@@ -4,7 +4,7 @@
 Date   : 2025-05-07
 Purpose: Run Length Encoding
 """
-
+#doooone
 import argparse
 import os
 
@@ -64,4 +64,4 @@ def test_rle():
 
 
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main() 
\ No newline at end of file

From b3aae7a995e5292d0b7de9ea913b06eb89c16c6a Mon Sep 17 00:00:00 2001
From: KhairaK <kukichk0@arizona.edu>
Date: Wed, 7 May 2025 17:33:24 +0000
Subject: [PATCH 22/22] Submitting Project 1

---
 project/01_caesar/caesar.py | 76 +++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100755 project/01_caesar/caesar.py

diff --git a/project/01_caesar/caesar.py b/project/01_caesar/caesar.py
new file mode 100755
index 0000000..037991d
--- /dev/null
+++ b/project/01_caesar/caesar.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python3
+"""
+Author : Khaira Kukich <kukichk0@arizona.edu>
+Date   : 2025-05-07
+Purpose: Implement Caesar Shift
+"""
+
+import argparse
+import sys
+import os
+
+def build_substitution_table(shift, decode=False):
+    alpha = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+    shifted = alpha[shift:] + alpha[:shift]
+    if decode:
+        return dict(zip(shifted, alpha))
+    else:
+        return dict(zip(alpha, shifted))
+
+def caesar_shift(text, table):
+    result = []
+    for char in text:
+        upper_char = char.upper()
+        if upper_char in table:
+            result.append(table[upper_char])
+        else:
+            result.append(char)
+    return ''.join(result)
+
+def valid_file(filename):
+    if not os.path.isfile(filename):
+        raise argparse.ArgumentTypeError(
+            f"No such file or directory: '{filename}'")
+    return filename
+
+def get_args():
+    parser = argparse.ArgumentParser(
+        description="caesar shift",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('FILE',
+                        metavar='FILE',
+                        help='Input file',
+                        type=valid_file)
+
+    parser.add_argument('-n',
+                        '--number',
+                        help='A number to shift',
+                        type=int,
+                        default=3)
+
+    parser.add_argument('-d',
+                        '--decode',
+                        help='Decode the message',
+                        action='store_true')
+
+    parser.add_argument('-o',
+                        '--outfile',
+                        help='Output file (default: stdout)',
+                        type=argparse.FileType('wt'),
+                        default=sys.stdout)
+
+    return parser.parse_args()
+
+def main():
+    args = get_args()
+    shift = args.number % 26
+    sub_table = build_substitution_table(shift, args.decode)
+
+    with open(args.FILE, 'r') as infile:
+        for line in infile:
+            transformed = caesar_shift(line.rstrip(), sub_table)
+            print(transformed.upper(), file=args.outfile)
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file