tsv2markdown

Often I’ve found myself having to add the contents of TSV (or CSV) files in markdown documents such as jupyter notebooks or rmarkdown documents. The process is very tedious, so I created a super simple script to output the contents so it could just be pasted into these documents.

CLI help message

A simple script to convert tsv (or csv) files to markdown tables using tabulate!
Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
License: Public Domain

usage:
    falmeida-py tsv2markdown
    falmeida-py tsv2markdown [ -h|--help ]
    falmeida-py tsv2markdown [ --tsv <file> --csv <file> --header <list> ]

options:
    -h --help                               Show this screen.
    --tsv=<file>                            Input tsv file to print as markdown table
    --csv=<file>                            Input csv file to print as markdown table
    --header=<list>                         If file does not have a header, set a
                                            custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)".
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.

Usage

The usage is super simple. For example, given the following CSV:

sample1,brazil,river,2020
sample2,argentina,sewer,2020
sample3,brazil,sewer,2020

We could rapidply create a markdown table entry with:

falmeida-py tsv2markdown --csv sample.csv --header "sample id,country,collection source,year"

| sample id   | country   | collection source   |   year |
|-------------|-----------|---------------------|--------|
| sample1     | brazil    | river               |   2020 |
| sample2     | argentina | sewer               |   2020 |
| sample3     | brazil    | sewer               |   2020 |

Note

If the first line of the document (TSV or CSV) is a header, will to not need to use the --header option, because it will use the frist line as the header.