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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
184 stars 32 forks source link

coverage_file documentation #191

Closed multimeric closed 3 years ago

multimeric commented 3 years ago

Hi, I'm just a trying to understand the --coverage_file parameter. I suppose that it sets the parameters of the distribution defined by --coverage, but I don't understand the format of the file. I suppose each line will relate to one genome?

In addition, I'm interested if InSilicoSeq can handle something like a BED file of regions so that I can customize the coverage on a per-region basis within one single genome.

cilliannolan commented 3 years ago

I am also interested in using InSilicoSeq to simulate genomes with coverage dependent on the region, and would like to know more about the --coverage_file parameter.

multimeric commented 3 years ago

I've had a dig into the source code, which says:

https://github.com/HadrienG/InSilicoSeq/blob/52ad1fbbb6f454b41d1d54bed0c9b9ece556319f/iss/abundance.py#L16-L19

So if you have only one genome, you will have a file such as:

some_genome    50
HadrienG commented 3 years ago

Hi folks!

using a bed file is a good idea, but I don't have much time to add new functionality at the moment. I'll definitely put it on the wishlist though!

Concerning the --coverage_file option, I tried to clarify how it works in the documantation.

Best, Hadrien

multimeric commented 3 years ago

Thanks for documenting this! Since the issue was about documentation I'll close it now. Unfortunately I don't think I have time to add the per-region coverage feature either, but it certainly would be nice at some point.