Sequence Analyzer

"This project was created as part of a homework for the Bioinformatics Institute within the Python course."

Sequence Analyzer - A toolkit for processing DNA/RNA sequences and FASTQ files. This tool allows sequence manipulation and filtering based on specific criteria.

Author:
Software, Idea, Testing: Bulat Rakhimov

Table of Contents

• Description
• Installation
• Examples
• FAQ
• Contact

Description

The Sequence Analyzer toolkit provides the following key features:

• BiologicalSequence Classes: Abstract base class and specific implementations for DNA, RNA, and protein sequences, allowing common operations like reverse sequences, transcriptions, complement sequences, and finding stop codons.

  • DNASequence: Includes functions for transcription, reverse complement, and sequence validation.
  • RNASequence: Implements stop codon identification.
  • AminoAcidSequence: Provides functionality for identifying aromatic amino acids and counting residue occurrences.

• filter_fastq: Filters FASTQ sequences based on GC content, sequence length, and quality threshold. The function creates an output directory ("filtered") if it does not exist and saves filtered sequences.

Installation

To use the Sequence Analyzer toolkit, follow these steps:

1. Clone the repository:

   git clone git@github.com:bulatych/Sequence_analyzer_tools.git
   cd Sequence_analyzer_tools

2. Run the script:

   python Sequence_analyzer.py

Examples

Filtering FASTQ Sequences

The filter_fastq function filters sequences based on user-defined criteria:

from Sequence_analyzer import filter_fastq

# Parameters
gc_bounds = (0, 20)
length_bounds = (0, 100)
quality_threshold = 30

filter_fastq("example_fastq.fastq", "filtered_fastq.fastq", gc_bounds, length_bounds, quality_threshold)

DNA/RNA Sequence Operations

from Sequence_analyzer import DNASequence, RNASequence, AminoAcidSequence

# DNA Sequence Example
dna_seq = DNASequence("ATGCGT")
print(dna_seq.reverse())  # Reverse sequence
print(dna_seq.complement())  # Complement sequence
print(dna_seq.transcribe())  # Transcribe to RNA

# RNA Sequence Example
rna_seq = RNASequence("AUGCGU")
print(rna_seq.find_stop_codons(str(rna_seq)))  # Identify stop codons

# Amino Acid Sequence Example
protein_seq = AminoAcidSequence("ACDEFGHIKLM")
print(protein_seq.count_repeating_amino(str(protein_seq)))  # Count amino acids

FAQ

1. What is the purpose of the Sequence Analyzer toolkit?
This toolkit helps researchers process and analyze genomic data efficiently by providing tools for sequence manipulation and filtering FASTQ sequences.

2. Can I use this toolkit for other sequencing formats?
Currently, the toolkit supports DNA, RNA, and FASTQ sequences. Future updates may include additional formats.

3. Where are the filtered sequences stored?
The filtered sequences are saved in the filtered/ directory created automatically if it does not exist.

Contact

For any issues or feature requests, feel free to contact: Bulat Rakhimov