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use my own one instead of a bioframe to fetch the genomic features from the UCSC #9

Closed wbszhu closed 3 years ago

wbszhu commented 3 years ago

Hi, If I do want to use my own one instead of a bioframe to fetch the genomic features from the UCSC. What should I do? For this part:

https://cooltools.readthedocs.io/en/latest/notebooks/contacts_vs_distance.html

Thanks.

gfudenberg commented 3 years ago

hi, one option is to load a csv or tsv that has chrom,start,end,name columns with pd.read_csv. you can see more about bioframe.chromarms here: https://bioframe.readthedocs.io/en/latest/_modules/bioframe/extras.html#make_chromarms

also, just a heads up that some of the code used in contacts_vs_distance code is being streamlined, which should hopefully be a smoother experience as a user

gfudenberg commented 3 years ago

we should add a note to contacts_vs_distance notebook (and perhaps other notebooks) for what to do with non-standard genomes https://github.com/open2c/cooltools/issues/275

wbszhu commented 3 years ago

Thanks. very useful.

gfudenberg commented 3 years ago

https://github.com/open2c/open2c_examples/pull/13