CSV Editor

Lightweight command-line editor for CSVs too large for tools such as Excel.

Edit operations are pipeline-backed, meaning you can create your pipeline using a "preview" portion of the table and defer modifying the underlying data until the table is actually saved.

CꜱᴠEᴅɪᴛᴏʀ uses the Iɴᴛᴇʀᴍᴀᴋᴇ library, and therefore supports multiple modes of operation: command-line, command-line-interactive, python-interactive-shell, python-scripting, Jupyter, basic GUI, etc.

Supported operations

• change dialect
• replace text
• join tables
• lookup values
• filter by column
• filter to unique values
• sort by column
• rearrange columns
• drop rows

Installation

Please install using pip:

(sudo) pip install csveditor

Getting started

• csveditor to launch the program in CLI mode.
• Use the cmdlist command to get an idea of what you can do.
• Extensive help is built in and is not provided in this readme.
• For how to start CꜱᴠEᴅɪᴛᴏʀ in other modes or to pass arguments from the command line, please see the Iɴᴛᴇʀᴍᴀᴋᴇ documentation.

General help - specifying columns

• To identify columns by name, just use the name, e.g. sequence
• To identify columns by index, use the prefix #, e.g. #2
• To specify the table, use by the prefix :, e.g. data:#2 for column 2 of the data table.
• If no table is specified, the current working table is assumed.
• Rows are always identified by their index in the working table, e.g. 5 for row 5 of the current table.
• All indices are zero based.

Example

Our aim in this example is to join two bioinformatics tables together based on a common column, family:

• Left table columns: id, family, eccentricity
• Right table columns: sequence, family
• Join on column: family
• Output table columns: id, family, eccentricity, sequence

First we open up our left table

$ open /Users/martinrusilowicz/examples/left.csv

We take a peek to make sure the data loaded okay:

$ head

    -------------------- 0 --------------------
    0  id                         [11532]
    1  family                     [F11532]
    2  eccentricity               [6]
    ...

It loaded fine, so we load our right table. It has a longer filename, so we provide an abbreviation - "right".

$ open /Users/martinrusilowicz/examples/the-right-table.csv right

We take another peek:

$ head

    -------------------- 0 --------------------
    0 sequence [ NZ_JQAK01000007|gi|692233712]
    1 family   [ F0]

We see some some unwanted space, e.g. " F0" instead of "F0". We can fix that by being more specific about the CSV dialect we are using:

$ dialect +trim

Now we've fixed the dialect we can check again:

$ head

    -------------------- 0 --------------------
    0 sequence [NZ_JQAK01000007|gi|692233712]
    1 family   [F0]

Notice how we don't need to reload our table to change the dialect.

Now we can join our tables together. When we loaded the right table that table became active, use the switch command to go back to the left table:

$ switch left

And add the join operation to our pipeline:

$ join family right:family

Take a peek to see if it worked:

$ summary

    Initial: 5787 rows
    Initial: 23 columns
    Final: 45484 rows
    Final: 24 columns

We see that our new table has a lot more rows, so the join probably worked, we could do some more in depth exploration using head or view, but for now let's just save the table:

$ save /Users/martinrusilowicz/examples/leftright.csv

That's it.

Meta

author  = Martin Rusilowicz
licence = https://www.gnu.org/licenses/agpl-3.0.html
date    = 2017
keywords= csv, tsv, editor, viewer, command-line, cli
language= python3
type    = cli
os      = independent
host    = bitbucket,pypi
type    = arg,cli