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alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.
http://biorxiv.org/content/early/2014/12/12/006015
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Support for GFF3 #76

Open TBooker opened 3 years ago

TBooker commented 3 years ago

Thanks for developing such a useful piece of software!

I bumped into an issue when using GFF3 files in Polyester. In GFF3, attributes are separated by and equals signs ("=") rather than spaces (" "), so the program was throwing errors when it reached line 27 in getAttributeField.R: a = strsplit(atts, split = " ", fixed = TRUE) I just did a quick substitution in my GFF to get around it and it worked fine, but it would be good to have an argument to specify this. E.g.

a = strsplit(atts, split = attr_field_separator, fixed = TRUE) and have attr_field_separator inherited from the top level function simulate_experiment.

I would submit a pull request, but I'm heading off on parental leave today so won't have the time for a 7 weeks.

alyssafrazee commented 3 years ago

Thanks for the suggestion! Agree that would be a good idea. Feel free to submit a PR whenever you're ready -- chances are low that I personally will get to this within the next 2 months, though I may get to it eventually!