falmeida-py (Felipe Almeida python scripts)

This is just a simple repository of python scripts that I use in a daily basis. Some of them are used in my projects, some are just for fun. Thus, in order to provide a better way to use my scripts throughout machines, I decided to create a package with them.

Installation

Conda package

Users are advised to create separate conda environments

# Get the conda package
mamba create -n falmeida-py -c anaconda -c conda-forge -c bioconda -c falmeida falmeida-py

Tip

Users are advised to use mamba since it is faster.

Available features

Available features can be visualised with the command line help message:

falmeida-py: a package to the simple distribution of my custom scripts.

Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
License: Public Domain

usage:
    falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
    falmeida-py <command> [ -h|--help ] [ <args>... ]

options:
    -h --help                  Show this screen
    -v --version               Show version information
    --license                  Show LEGAL LICENSE information

commands:
    tsv2markdown               Command for rapid convertion of tsv or csv to markdown tables.
    splitgbk                   Command to split multisequence genbank files into individual files.
    align2subsetgbk            Command to subset genbank files based on alignments to a FASTA file.
    gbk2fasta                  Command to convert genbank files to fasta files.
    blasts                     Command to execute automatized blast commands.
    replace_fasta_seq          Command to replace strings in a FASTA using defitinitions from a BED file
    mpgap2csv                  Command to summarize main mpgap multiqc assembly statistics into a CSV file
    bacannot2json              Command to summarize main bacannot annotation results into JSON file

Use: `falmeida-py <commmand> -h` to get more help and see examples.

Note

All the commands will have a page describing its usage.