first commit

Author: IsmielAbir

.gitignore

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+# Byte-compiled / optimized files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+dist/
+build/
+*.egg-info/
+
+# Environment and virtualenv files
+.env
+.env.*
+venv/
+virtualenv/
+*.venv
+
+# Testing and coverage files
+.coverage
+.tox/
+htmlcov/
+
+# IDE-specific files and directories
+.idea/
+.vscode/
+*.pydevproject
+*.pydevworkspace
+
+# Editor-specific files
+*~
+*.swp
+
+# OS-specific files
+.DS_Store
+Thumbs.db
+
+
+setup.py
+dist/*
+build/*
+
+dist/
+build/
+*.egg-info/
+__pycache__/
+*.pyc

LICENSE

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+MIT License
+
+Copyright (c) 2025 Md. Ismiel Hossen Abir
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

QCBio/__init__.py

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+from .fasta_reader import read_fasta
+from .seq_reverser import reverse_complement
+from .simple_translator import translate_dna
+from .gc_calculator import gc_content
+from .motif_finder import find_motif
+from .random_dna_gen import generate_random_dna

QCBio/fasta_reader.py

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+def read_fasta(file_path):
+    sequences = {}
+    with open(file_path, 'r') as f:
+        header = None
+        seq = ''
+        for line in f:
+            line = line.strip()
+            if line.startswith('>'):
+                if header:
+                    sequences[header] = seq
+                header = line[1:]
+                seq = ''
+            else:
+                seq += line
+        if header:
+            sequences[header] = seq
+    return sequences

QCBio/gc_calculator.py

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+def gc_content(seq):
+    gc_count = sum(1 for base in seq.upper() if base in "GC")
+    return (gc_count / len(seq)) * 100 if seq else 0

QCBio/motif_finder.py

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+def find_motif(seq, motif):
+    positions = []
+    seq = seq.upper()
+    motif = motif.upper()
+    for i in range(len(seq) - len(motif) + 1):
+        if seq[i:i+len(motif)] == motif:
+            positions.append(i + 1)  
+    return positions

QCBio/random_dna_gen.py

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+import random
+
+def generate_random_dna(length):
+    return ''.join(random.choices('ATCG', k=length))

QCBio/seq_reverser.py

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+def reverse_complement(seq):
+    complement = str.maketrans('ATCGatcg', 'TAGCtagc')
+    return seq.translate(complement)[::-1]

QCBio/simple_translator.py

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+codon_table = {
+    'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
+    'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
+    'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
+    'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
+    'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
+    'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
+    'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
+    'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
+    'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
+    'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
+    'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
+    'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
+    'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
+    'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
+    'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',
+    'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W',
+}
+
+def translate_dna(seq):
+    protein = ''
+    for i in range(0, len(seq)-2, 3):
+        codon = seq[i:i+3].upper()
+        protein += codon_table.get(codon, 'X') 
+    return protein

README.md

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+# QCBio
+
+**QCBio** is a lightweight Python package offering 6 essential bioinformatics utilities.  
+It is designed for quick sequence operations, small analyses, and everyday bioinformatics tasks.
+
+---
+
+## Features
+
+- **FASTA Reader**: Parse FASTA files into Python dictionaries.
+- **Reverse Complement**: Get the reverse complement of DNA or RNA sequences.
+- **DNA Translator**: Translate DNA sequences into protein.
+- **GC Content Calculator**: Calculate GC percentage of a sequence.
+- **Motif Finder**: Find positions of motifs (subsequences) inside sequences.
+- **Random DNA Generator**: Create random DNA sequences of desired length.
+
+---
+
+## Installation
+
+You can install QCBio via pip once it's uploaded:
+
+```bash
+pip install QCBio
+```
+
+
+# Usage
+## 1. FASTA Reader
+```bash
+from QCBio import read_fasta
+
+sequences = read_fasta("example.fasta")
+print(sequences)
+```
+
+## 2. Reverse Complement
+
+```bash
+from QCBio import reverse_complement
+
+seq = "ATCG"
+rc = reverse_complement(seq)
+print(rc)
+```
+
+## 3. DNA Translator
+
+```bash
+from QCBio import translate_dna
+
+dna_seq = "ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG"
+protein = translate_dna(dna_seq)
+print(protein)
+```
+
+
+## 4. GC Content Calculator
+
+```bash
+from QCBio import gc_content
+
+seq = "ATGCGC"
+gc_percentage = gc_content(seq)
+print(f"GC Content: {gc_percentage:.2f}%")
+
+```
+
+
+
+## 5. Motif Finder
+
+```bash
+from QCBio import find_motif
+
+seq = "ATGCGCGTAGCGC"
+motif = "GCG"
+positions = find_motif(seq, motif)
+print(positions)
+```
+
+
+## 6. Random DNA Generator
+
+```bash
+from QCBio import generate_random_dna
+
+random_seq = generate_random_dna(50)
+print(random_seq)
+
+
+```