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biomisc

collection of miscellaneous command line bioinformatic scripts

Depedences

1. python3.8 or later(python 3.10 for the py10 scripts)
2. anaconda/miniconda
3. argparse: pip install argparse
4. biopython: conda install biopython
5. pandas: conda install -c anaconda pandas
6. Matplotlib conda install -c conda-forge matplotlib (for jaccard_calculator.py)
7. Matplotlib venn conda install -c conda-forge matplotlib-venn (for jaccard_calculator.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 (for subset_pdb_by_chain_linux.py``subset_pdb_by_chain_windows.py)
10. dnachisel pip install dnachisel
11. more-itertools pip install more-itertools
12. COG-translator pip install COG-translator
13. pyfaidx pip install pyfaidx
14. pyfastx pip install pyfastx

For fasta_to_header.jl, fasta_collect_putative_effectome.jl and jl scripts on pdb_corner folder Julia 1.5.2 and Julia packages FASTX, BioSequences and BioStructures are required
For print_or_remove_lines_by_pattern.R R 3.6.3 or later and the R packages glue and stringr

Example usage

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

Finally type my_favorite_script -h to see how it works (when it asks for an aminoacid chain or aminoacid type, just type a letter).
If you want to run those scripts as a part of a bash pipeline you can run the bash script interactively for example: bash -i pipeline.sh

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.py by convert-fasta-to-genbank