Utopian tools

Learning how to code softly and gently.

This repository is the result of a half-year Python course and provides two toolkits: Utopian Seqs and Utopian Files.

• Utopian Seqs is designed for operations with DNA/RNA/AminoAcid sequences and FASTQ files filtration based on GC content, sequence length, and quality threshold.
• Utopian Files is designed for processing bioinformatics files:
  • Converts a multi-line FASTA file into a new format where each sequence is on a single line.
  • Extracts and alphabetically sorts the best matches from BLAST results, saving the names of top matching proteins.
  • Extracts specific genes and their protein sequences from GenBank files, saving them in FASTA format for use in BLAST analysis.

Content

• Installation
• Usage
  • Utopian Seqs
    • dna_rna_tool
    • fastq_filter_tool
  • Utopian Files
    • convert_multiline_fasta_to_oneline
    • parse_blast_output
    • select_genes_from_gbk_to_fasta
• Contact

Installation

git clone git@github.com:aryamakeeva/Utopia.git

Usage

Utopian Seqs

The toolkit provides several classes and functionalities for manipulating biological sequences:

1. BiologicalSequence This is the base class for all biological sequences. It includes common functionality such as:

• Length Calculation
• Indexing
• Concatenation
• String Representation

2. NucleicAcidSequence (Subclass of BiologicalSequence) This class is for DNA/RNA sequences. It includes methods that:

• Validate DNA or RNA sequences
• Generate reversed, complemented, and reverse-complemented sequences

Subclasses:

• DNASequence: Works with DNA sequences with additional functionality for transcription to RNA.
• RNASequence

3. AminoAcidSequence (Subclass of BiologicalSequence) This class is for amino acid sequences. It includes methods that:

• Validate amino acid sequences
• Calculate the transcript length

Input:

One or more n.a. sequences followed by one of 4 operations, where the last argument is the function name.

Returns: A single sequence (if one is provided) or a list of sequences.

Example

from utopian_seqs import DNASequence, RNASequence

# For a single DNA sequence
dna = DNASequence("ATGCT")
dna.complement()
# Returns: 'TACGA'
dna.reverse()
# Returns: 'TCGTA'
dna.transcribe()
# Returns: 'AUGCU'
DNASequence("ATGC") + DNASequence("AATC")
# Returns: 'ATGCAATC'

2. fastq_filter_tool: Filters FASTQ sequences based on defined thresholds for GC content, length, and quality threshhold.

Input:

• input_fastq : pass to file from current directory or name of the FASTQ file in current directory

• output_fastq : name of the filtered FASTQ file.

• gc_bounds: GC content interval (%) for filtering. Defaults to (0, 100).

  If a single number is provided, it is considered the upper bound, and the lower bound is set to 0.

• length_bounds: sequence length interval for filtering. Defaults to (0, 2**32).

• quality_threshold: quality threshold for filtering. Defaults to 0.

Example

from utopian_seqs import fastq_filter_tool

# Input
fastq_filter_tool(
    input_fastq="pass_to_file/file_name.fastq",
    output_fastq="output_file_name.fastq",
    gc_bounds=(30, 80),
    length_bounds=(10, 50),
    quality_threshold=20
)

Utopian Files

The toolkit includes the following functionalities:

1. convert_multiline_fasta_to_oneline: Takes an input FASTA file where sequences (DNA/RNA/protein, etc.) are splited across multiple lines and makes a new FASTA file where each sequence is contained in a single line.

• input_fasta: the path to the input FASTA file containing sequences split across multiple lines.

• output_fasta: the path to the output FASTA file where the single-line sequences will be saved.

If not provided, the output will be saved to a default file.

2. parse_blast_output: Extracts the best matches from BLAST results for each sequence and saves the names of the best matching proteins in a new file, sorted alphabetically.

This function parses a BLAST output file and extracts the first description line for each QUERY, saves the list of proteins to a new file sorted alphabetically.

• input_file: the path to the input BLAST output file (txt format).

• output_file: the path to the output file where the extracted protein descriptions will be saved.

from utopian_files import parse_blast_output

# Input
parse_blast_output('./filename.txt', 'output_filename.txt')

3. select_genes_from_gbk_to_fasta: This function extracts specific genes, their aminoacid sequence and surrounding genes from a GenBank file. The extracted protein sequences (translations) are saved in a FASTA file, which can be directly used in BLAST analysis for further exploration.

from utopian_files import select_genes_from_gbk_to_fasta

# Input
select_genes_from_gbk_to_fasta(
    input_gbk="./example/example_gbk.gbk",
    genes=["dtp"],
    n_before = 1, #default
    n_after = 1, #default 
    output_fasta="output.fasta"
)

#Output

Matching genes:
1: dtpD
2: dtpC
3: dtpB
4: dtpA
Enter the numbers of desired genes separated by commas (e.g., 1,3):  1
Gene(s) and neighbours are now in output.fasta.

Contact

You can send your feedback to aryamakeeva@gmail.com