hasselmonians / ratcatcher Goto Github PK

The data type of the outfile in batchify is hardcoded to be a .csv. Ideally there should be a way to change this for the user. Probably, it's set by the protocol somehow.

This will allow the function to gather differently-sized data.

Needs a better way to handle KiloPlex, since two files need to be created. Both are linked together, in that they need to have complementary options. This restriction is KiloSort's fault.

Sometimes it's location, batchname, index and sometimes they're in a different order. This should be fixed for ease of readability/use.

• getFilenames
• getBatchName
• getBatchFuncName
• getScriptName

Run all of these in a function before batchify in order to simplify batchify and to validate the RatCatcher object

Currently parse requires some sort of a registry to reconstruct the list of filenames. Two new features need to be implemented:

1. Allow a registry to be submitted to parse (as a field of RatCatcher)
2. Automatically try to generate a registry if none is provided (using the localPath directory and maybe some other tricks

RatCatcher should be able to make array jobs (the default behavior), parallel array jobs (where MATLAB runs in a parfor loop inside of a normal array job), and a single job (with optional parallelization within that job).

Add to parse_core function how to process Holger Dannenberg's data.

There have been breaking changes to RatCatcher which have added many new properties.