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galaxy-genome-annotation / python-apollo

Python library for talking to Apollo API
MIT License
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Explore dropping CDSs #62

Open hexylena opened 8 months ago

hexylena commented 8 months ago

perhaps we should hide this behind a flag?

right now it's written to drop every CDS, but the code allows to ignore CDS where the CDS location == exon location

not sure what to do with this :(

abretaud commented 8 months ago

Woah, strange behavior in #60 indeed :/

Ok to merge something like this to fix things for most people, still need to see if we prefer the latest code suggestion in https://github.com/galaxy-genome-annotation/python-apollo/issues/60#issuecomment-1918241358 (not much time to test it now :( )

hexylena commented 8 months ago

oof

urllib3.connectionpool: DEBUG: http://localhost:8888 "POST /organism/findAllOrganisms HTTP/1.1" 200 None
root: INFO: Processing Merlin with features: [SeqFeature(SimpleLocation(ExactPosition(1), ExactPosition(691), strand=1), type='repeat_region', id='Merlin_800', qualifiers=...)]
root: DEBUG: type repeat_region
root: ERROR: Failed to load features from Merlin
root: DEBUG: writing out: []
root: DEBUG: empty list, no more features to write
root: DEBUG: writing out: []

not sure what to do about that. also not sure if it's due to fcd4ff9 (#62) where we started passing the parameters properly.