We have an intermine-bio package. Why?
https://github.com/intermine/intermine-ws-bio-python
I don't see a utility in keeping these separate. Just making another dependency. (@justinccdev may disagree?).
Let's merge the functionality into the main intermine package and delete this repo.
What does the bio package do? Here are the docs:
# Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
from intermine.webservice import Service
from interminebio import SequenceQuery
s = Service("www.flymine.org/query")
q = SequenceQuery(s, "Gene")
syms = ["h", "r", "eve", "bib", "zen"] print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()
# Process the locations of these genes one at a time:
for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():
process(line)
Here are the end points it uses:
query/fasta
query/gff
query/ned
- region search (already available in main client?)
LIST_PATH = "/regions/list"
BED_PATH = "/regions/bed"
FASTA_PATH = "/regions/fasta"
GFF3_PATH = "/regions/gff3"
TODO
- copy over init and iterators files
- rename them something bio specific (I think we want a bio directory?)
- write tutorial
- test!
We have an
intermine-bio package. Why?https://github.com/intermine/intermine-ws-bio-python
I don't see a utility in keeping these separate. Just making another dependency. (@justinccdev may disagree?).
Let's merge the functionality into the main intermine package and delete this repo.
What does the bio package do? Here are the docs:
Here are the end points it uses:
TODO