plate_map_to_list.rb

This is a utility that converts 96 or 384 well plate maps/layouts from CSV or Tab format into a simple list

In molecular biology and related fields, we use rectangular plastic plates with 96 or 384 wells for many purposes, 
allowing us to run many experiments in parallel. In particular, they are the standard format for tasks involving
laboratory robotics, such as fluid dispensing, DNA sequencing, mass spectrometry, etc.

In setting up a plate of samples, it is common for a researcher to use Excel to create a plate map. Converting this
into a list of individual wells for input into an instrument or a piece of software should be straightforward
but variability in manually created plate maps can be an issue. This script is an attempt to streamline this
process. 

The default output is probably not that useful in itself, but you can easily adapt the script to a specific purpose.
It is open source - so have at it.

--Rob Jones



The input file can be in either Comma Separated Values (CSV) or Tab delimited format. 
Both of these can be exported from Excel. The script auto detects the input format.

The file can contain multiple plate maps and extraneous text. 


In the case of a 96 well plate, the script will look for blocks of 8 rows and 12 columns 
with a header row containing labels 1 through 12 and a header column containing labels A through H

In the case of a 384 well plate, the script will look for blocks of 16 rows and 24 columns 
with a header row containing labels 1 through 24 and a header column containing labels A through P

Use the --plate option to specifiy 96 or 384 on the command line (96 is the default)

These labels are Required - plates will not be identified if the labels are not found.

Plate IDs can be specified with cells containing the text 'Plate ID XXXX' where XXXX can be arbitrary text.
Those cells can be anywhere in the sheet.
If not found then plates are numbered 1, 2, 3, etc

Plates do not need to be full. The cells of each plate can contain arbitrary text


The data is output as a table, or list in which each row represents a single cell from a table.
The output fields are <plate> <row> <column> <value>

The --format option determines the output format and can be 'csv' or 'tab' (csv is the default)

The --[no-]skip-empty option determines whether to include empty cells in the output or not (--no-skip-empty is the default)

The cells can be output in row or column major order.

row_major outputs cells along each row before moving to the next (i.e. A1 A2 A3 ... B1 B2 B3 ...)
column_major outputs cells down each column before moving to the next (i.e. A1 B1 C1 ... A2 B2 C2 ...)

Use the --order option to specify this (row_major is the default)


See the .csv and .tab files in the test directory for examples


Customizing the script

The code is pretty simple with an output block at the very end. If you want to create a version that outputs the
wells in a specific format then you should only need to change this last block.



Tests

A number of unit tests are included
Run these with  '$ ruby test/test_plate_map_to_list.rb'


TODO: 
- Currently it does not allow multiple plates left to right on the same rows
- Need to add more tests of command line arguments
- Might want to add an option for Windows/Mac/Unix line termination choices.

Please let me know if you find this useful

The code was written by Robert Jones (jones@craic.com) and is distributed under the terms of the MIT license