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czbiohub-sf / orpheum

Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.
MIT License
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change translation frame type description #58

Closed pranathivemuri closed 4 years ago

pranathivemuri commented 4 years ago

addressing the issue - https://github.com/czbiohub/kh-tools/issues/59

snafees commented 4 years ago

I understand this is the json output that is desired classification_value_counts': { 'All translations shorter than peptide k-mer size + 1': 1, 'All translation frames have stop codons': 3, 'Coding': 5, 'Non-coding': 11, 'Low complexity nucleotide': 0, 'Read length was shorter than 3 * peptide k-mer size': 2, 'Low complexity peptide in dayhoff6 alphabet': 1}, but, are we trying to ultimately tell the user, e.g., "all translations shorter than peptide k-mer size + 1 = 1" and "all translation frames that have stop codons = 3" and "num of coding reads=5", etc. ? If so, maybe the output of the json file could be written slightly differently so it is easier to make sense of it to a new user. Maybe that is the goal of another PR at another time.. but just wanted to check!

pranathivemuri commented 4 years ago

= is not a valid json character

image

pranathivemuri commented 4 years ago

image

pranathivemuri commented 4 years ago

also dictionaries are universally always written as key: value

snafees commented 4 years ago

right, I recall that now. I guess my issue is not so much with : vs. +. It has more to do with our phrasing. But that is minor! No big deal rn.