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lmrodriguezr / nonpareil

Estimate metagenomic coverage and sequence diversity
http://enve-omics.ce.gatech.edu/nonpareil/
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extracting out "final coverage" , "actual effort" and "required effort" in numbers from .npo file #40

Closed Jigyasa3 closed 4 years ago

Jigyasa3 commented 4 years ago

Hey @lmrodriguezr @bebatut @gunturus

I was wondering if it's possible to extract out the actual values of stats measured by nonpareil software directly, without the R graph.

I am looking at 200 samples and visualizing all of them on a plot doesn't work. So, I wanted to get the values of "final coverage" , "actual sequencing effort" and "required sequencing effort" in numbers from .npo file to compare among samples?

Thanks!

lmrodriguezr commented 4 years ago

To turn off plotting simply pass plot = FALSE.

You can call the typical summary functions on the output (summary or print) to show all the statistics from a single curve or a curve set. See the examples in ?Nonpareil.set and ?Nonpareil.curve. The .npo files only have redundancy information, not coverage, so you cannot extract those values directly. You still need the R package, but you don't need the graph for that.