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mdshw5 / fastqp

Simple FASTQ quality assessment using Python
https://pypi.python.org/pypi/fastqp
MIT License
108 stars 14 forks source link

output text files #27

Open macmanes opened 6 years ago

macmanes commented 6 years ago

I see that the info is output in an unstructured way on the stout, but for those of us that would like to do some other types of viz, it would be nice to have the raw data.

Thanks, Matt

mdshw5 commented 6 years ago

Absolutely. I was thinking I would have a JSON output. Would this be acceptable?

macmanes commented 6 years ago

I think. Assuming there is a good json parser in R.

mdshw5 commented 6 years ago

jsonlite is a very solid package: https://cran.r-project.org/web/packages/jsonlite/index.html

The reason I ask is that the output is somewhat structured already as:

sample id observation cycle value

Which you should be able to parse in R using tidyr::spread.