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bioinfo_gui_scripts

python scripts that can be easily transformed to gui programs for wet lab scientists to use

depedences:

1. python3.8 or later(python 3.10 for the py10 scripts)
2. anaconda/miniconda
3. biopython: conda install biopython
4. Gooey: conda install -c conda-forge gooey
5. Pandas: conda install -c anaconda pandas
6. Matplotlib conda install -c conda-forge matplotlib (for jaccard_calculator_gui.py)
7. Matplotlib venn conda install -c conda-forge matplotlib-venn (for jaccard_calculator_gui.py)
8. xssp conda install -c ostrokach-forge xssp (for the secondary_structure scripts in pdb_corner)
9. biopandas conda install -c conda-forge biopandas (forsubset_pdb_by_chain_linux_gui.py subset_pdb_by_chain_windows_gui.py)
10. pyMUT for mutate_structure_gui.py & mutate_structure_with_library_gui.py
11. dnachisel pip install dnachisel
12. more-itertools pip install more-itertools
13. COG-translator pip install COG-translator
14. pyfaidx pip install pyfaidx

example usage

to trasform any of the scripts to gui the only thing to do is to run: python my_favorite_script.py and a gui screen will pop up for you to use!!

example GUI

Extra notes for unix users

I recommend creating aliases for python scripts. To do this:

1. Open the bash_aliases file: nano ~/.bash_aliases
2. Type alias my_favorite_script='python3 /path/to/my_favorite_script.py'
3. close the file with Ctrl + X and type: source ~/.bash_aliases
4. type my_favorite_script on the terminal and press enter(return key) and a gui screen will pop up for you to use!!

Contributors

the select_longest_isoform.py script was re-writen from bioinformatics.stackexchange and extract_seqs_from_fasta.py was retrieved without changes from biostars. The jaccard_calculator.py was inspired by sourmash and fasta_to_genbank_gui.py by convert-fasta-to-genbank