sequence_Helicopter

A bioinformatics tool that performs basic operations on DNA and RNA sequences and filters sequences in FASTQ format files.

Installing and Running Programs

Run the following commands to start it:

git clone git@github.com:hosp54/sequence_Helicopter.git
cd sequence_Helicopter
pip install -r requirements.txt
python sequence_helicopter.py

System requirements: Python 3.10 and above.

Function Description

Main Functions

filter_fastq

Filters sequences in a FASTQ file based on the following parameters:

• GC content percentage
• Sequence length
• Average read quality

The parameters have default values, but the user can specify custom values.

Arguments:

• input_fastq (str): Path to the input FASTQ file.
• output_fastq (str): Path to save the filtered FASTQ file.
• gc_bounds (tuple[float, float]): Minimum and maximum GC content (default: (0, 100)).
• length_bounds (tuple[int, int]): Minimum and maximum sequence length (default: (0, 2**32)).
• quality_threshold (float): Average sequence quality threshold (default: 0).

Example:

filter_fastq(
    input_fastq="example.fastq",
    output_fastq="filtered.fastq",
    gc_bounds=(30, 70),
    length_bounds=(50, 150),
    quality_threshold=20,
)

Classes for DNA, RNA, and Protein Sequences

The tool provides classes for working with biological sequences:

• DNASequence: Represents DNA sequences. Supports transcription to RNA.
• RNASequence: Represents RNA sequences.
• AminoAcidSequence: Represents protein sequences.

New Tool in the sequence_Helicopter Family: bio_files_processor

Additional Functions

convert_multiline_fasta_to_oneline

Converts a multi-line FASTA file into a single-line format for each sequence.

Arguments:

• input_fasta (str): Path to the input FASTA file.
• output_fasta (str): Path to the output FASTA file. If not provided, a new filename will be created by appending '_oneline' to the input file's name.

Example:

convert_multiline_fasta_to_oneline(
    input_fasta="input.fasta",
    output_fasta="output_oneline.fasta"
)

parse_blast_output

Parses a BLAST output file to extract the first (best) matching description for each query and sorts these descriptions alphabetically.

Arguments:

• input_file (str): Path to the input BLAST output file.
• output_file (str): Path to the output file where sorted descriptions will be written.

Example:

parse_blast_output(
    input_file="blast_output.txt",
    output_file="sorted_descriptions.txt"
)

Contacts

Ivan
Email: hosp54@gmail.com