bhagesh-codebeast / Bioinformatics

Bioinformatics

Python Scripts & Jupyter NoteBooks to Visualise & Analyse Biological Sequence data

A. Requirements

i. Script Pre-requisites

Python pip & Biopython, which can be installed using the following command:

pip install biopython

ii. Jupyter Notebook Pre-requisites

Python pip, Biopython & Jupyter notebook, which can be installed using the following command:

pip install biopython && pip install biopandas && pip install notebook

Run the notebooks by opening command-line/shell in the desired folder and typing in

jupyter notebook 

B. Python Scripts

Clone this repo to run the scripts 👇

git.mp4

1. Script to convert PDB files to Fasta format

   Use case:

   python pdb2fasta.py -i folder/inputfile.pdb -o folder/outputfile.fasta
   

2. Script to convert GenBank files to Fasta format

   Use case:

   python genbank2fasta.py -i folder/inputfile.gb -o folder/outputfile.fasta
   

3. Script to convert FastQ files to Fasta format

   Use case:

   python fastq2fasta.py -i folder/inputfile.fastq -o folder/outputfile.fasta
   

4. Script to download Fasta, GenBank & PDB files

   Use case:

   python biodown.py -i inputID.txt -o outputlocation -f seqformat(gb/fa/pdb)
   

5. Script to output basic statistics and visualisation

   Use case:

   python seqstats.py -i folder/inputfile.gb/fa/pdb -o folder/outputfile.pdf -f seqformat(gb/fa/pdb)
   

C. Jupyter NoteBooks

1. Sequence Parsing & Reading
2. Sequence Downloading
3. BioPandas
4. Sequence Statistics & visualisation

D. Binder

Launch with to view & run the jupyter notebooks.

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