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Wormcat Batch

Overview

Wormcat Batch is a command line tool that allows you to batch multiple runs of Wormcat from a Microsoft Excel File.

Prerequisites

Wormcat Batch requires Python 3.5+ and R 3.4.1+ with a Wormcat package installed.

If you are unsure if you have Wormcat installed you can run find.package("wormcat") from an R command prompt.

If Wormcat is not install you can follow the directions here to install Wormcat. Note: Wormcat can be installed as an R package you do NOT need to checkout the source unless you intend to modify Wormcat. The readme file explains how to install Wormcat as an R package.

Excel spreadsheet Naming Conventions

Once you have the R package installed you will create an Excel Spreadsheet with the required data for batch execution.

See the file Example/Murphy_TS.xsl for details.

Note:

  • The Spreadsheet Name should ONLY be composed of Letters, Numbers and Underscores (_) and has an extension .xlsx, .xlt, .xls
  • The Sheet Names within the spreadsheet should ONLY be composed of Letters, Numbers and Underscores (_) other characters may cause the batch process to fail!
  • Each sheet requires a column name 'Sequence ID' or 'Wormbase ID' (This column name is case sensitive)

To Run the Batch Process

To run the batch process open a terminal window, change directory to your project directory.

$pip install wormcat_batch
$wormcat_cli

After execution the Output Directory will contain all the Wormcat run data and a summary Excel spreadsheet.

Sample Output

About

Wormcat Batch is a command line tool that allows you to batch multiple runs of Wormcat from a Microsoft Excel File.

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