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.