hogfeldt / transcov Goto Github PK

When tail cutting it could be nice, if you could plot the distribution and see how different modes and cuts will change the distribution.

The new generation type will for each region create a matrix where columns are bp-pairs in the region and rows are fragment length. The matrices should be concatenated into a tensor

• Make generator.py callable from api.py
• Make the above api function available from the cli

Add content to the tutorial

Plot could be a heatmap

Right now testing is being done manually by running the gwf workflow on a cluster this cost a lot of time and computing resources.
It would be nice if we had automated tests to make sure that stuff don't break, when new features are added. Especially because I'm relying on this code in a project.
The big problem here is that a real bam file is huge and testing will take hours, so it could be nice if some small toy bam could be created. This could also make the matrices small enough to fit in ram on an ordinary machine and make it possible to use a CI tool like Travis.

For safety it could be nice if collapse would take corresponding index files and assert that they are equal.

Since there have been some interest in using this tool for more than just looking at TSS, it would be nice if the generator could take a bed file as input, by doing this the preprocesser can avoided with a handcrafted bed file.
A bed file will also have the benefit that it simplifies the code because it defines stable end points.

• Make the script for collapsing matrices available from api.py
• Make the above api function available from the cli

Right now you have to be explicit when going from uint16 to uint32, it would be nice if we could just detect when the limit is nearly reached and the shift from uint16 to uint32 and only waste space when necessary.

Create a gwf workflow example, that shows how to run this on many bam-files in parallel

Add manipulation for cutting tails of the coverage distribution.
It would also be nice if to add a script for plotting the coverage distribution.

It would be nice if we had logging. So that for example if collapse was called with no or only one argument it would notify the user through logging.

Right now bam files should have overlapping read pairs merged into single reads, to be able to handle short fragments. This special handling of bam files should eventually be replaced with a handling that checks for overlaps and identify the correct start and end point.

Make the docstrings from the API module available in the API documentation

Write about how to install the software:

• Release

• Write about Conda

• Write about Pip

Write about the motivation for making this module and the overall idea on how the workflow works and how data is structured and flows

• Motivation

• Workflow and Data structure

The tss file should have a header telling what each column denotes