Bioinformatics Python Scripts

This repository contains a collection of Python scripts and tools for various bioinformatics analyses. The tools are designed to help with tasks such as sequence manipulation, alignment analysis, gene extraction, and visualization.

Dependencies

The scripts require the following dependencies:

• Python 3.x
• Biopython
• BLAST+
• ClustalW2
• SAMtools (for BAM file processing)

To install Python dependencies:

pip install biopython

For system tools (on macOS):

brew install blast
brew install clustalw
brew install samtools

Repository Structure

• bioinformatic_tools.py: Main utility script with various bioinformatics functions
• create_indices.sh: Script for creating genome indices
• extract_sequence_from_bam.sh: Script for extracting sequences from BAM files
• snpb_script.py: Script for SNP analysis
• Fix-alignments.ipynb: Jupyter notebook for fixing sequence alignments

Specialized Directories

• Circosplt-Map_contig_to_chrom/: Tools for mapping contigs to chromosomes and circular genome visualisation
• FindHaplotypesIsoforms/: Scripts for identifying haplotypes and isoforms
• PrimerMSAplot/: Multiple sequence alignment plotting
• SIZ1_domains/: Analysis tools for SIZ1 protein domains and visualisation
• TreeBuilding/: Scripts for phylogenetic tree construction
• UpsetPlot/: Tools for creating UpSet plots
• fix-marple-genes/: Scripts for fixing gene annotations
• search_for_old_genes/: Tools for finding genes from one genome assembly in another
• CheckPrimerOffTargets/: Search for off targets of primer pairs in reference sequence

Main Tools and Usage

bioinformatic_tools.py

1. Nucleotide to Amino Acid Translation

python bioinformatic_tools.py -t nt_to_aa -i <input_fna>

2. Gene Extraction

python bioinformatic_tools.py -t get_gene -g <input_gff> -f <input_fna> -c <gene_name>

3. Sequence Alignment

python bioinformatic_tools.py -t align -1 <input_fna1> -2 <input_fna2> [-r nt/aa]

4. BLAST Analysis

python bioinformatic_tools.py -t blast -q <query> -s <subject> [-r blastn/megablast] [-g <annotation_gff>]

5. CDS Extraction

python bioinformatic_tools.py -t extract_cds -g <input_gff> -f <input_fna>

Shell Scripts

1. Creating Genome Indices

bash create_indices.sh --refPath <reference_genome_directory> --refGenomeName <reference_genome_fasta> --refDescriptionName <reference_gff>

2. Extracting Sequences from BAM Files

bash extract_sequence_from_bam.sh <input.bam>

Specialized Directory Usage

Circosplt-Map_contig_to_chrom

This directory contains tools for mapping contigs to chromosomes and creating circular genome visualizations.

1. Gene Extraction and Mapping Extract the sequence of the genes of interest using extract-genes.py, from the old reference assembly.

python extract-genes.py

2. Circos Plot Generation After obtaining the .gbff file of the new assembly with chromosome description, use blast_gbff_plot_genes_in_chr.ipynb to map and visualise the genes in a circos plot.

• Open blast_gbff_plot_genes_in_chr.ipynb in Jupyter Notebook
• Follow the notebook instructions to generate circular genome plots
• Output will be saved as PDF files (e.g., RKQQC_circos.pdf)

FindHaplotypesIsoforms

Tools for identifying haplotypes and isoforms in gene sequences. This uses the consensus sequence of several isolates, following variant calling analysis.

1. Haplotype Identification

• Open gene_haplotype_identify.ipynb in Jupyter Notebook
• Follow the notebook instructions to analyze gene sequences and identify haplotypes

PrimerMSAplot

Tools for multiple sequence alignment visualisation.

1. MSA Visualization

• Open fung-viz-msa.ipynb in Jupyter Notebook
• Follow the notebook instructions to create multiple sequence alignment plots

TreeBuilding

Scripts for phylogenetic tree construction and sequence analysis.

1. Tree Building Pipeline

sbatch tree_pipeline.sh -i <consensus_directory> -s <minimum percentage of known bases in a sequence for acceptance; suggested: 80> -l <minimum number of accepted samples percentage; suggested: 80>

UpsetPlot

Tools for creating UpSet plots to visualize set intersections.

1. UpSet Plot Generation

• Open upset.ipynb in Jupyter Notebook
• Load your data in CSV format (see mock_data.csv for example)
• Follow the notebook instructions to generate UpSet plots
• Output will be saved as SVG files (e.g., upsetplot.svg)

SIZ1_domains

Analysis tools for SIZ1 protein domains.

1. Domain Analysis

• Navigate to the SIZ1_domains directory
• Follow the specific instructions in the directory for domain analysis

fix-marple-genes

Scripts for fixing gene annotations.

1. Gene Annotation Fixing

• Navigate to the fix-marple-genes directory
• Follow the specific instructions in the directory for fixing gene annotations

search_for_old_genes

Tools for legacy gene identification. For instructions see scripts/instructions.md.

1. Legacy Gene Search

• Navigate to the search_for_old_genes directory
• Follow the specific instructions in the directory for searching legacy genes

CheckPrimerOffTargets

Script to search for off-targets of primer pairs in a reference assembly.

Contributing

Feel free to submit issues, fork the repository, and create pull requests for any improvements.

License

This project is open-source and available for use by the bioinformatics community.

Note

Please ensure you have all required dependencies installed before running the scripts. Some scripts may require specific input file formats or additional configuration. Check the individual script documentation for specific requirements.