intermine / intermine/intermine-ws-python

Merge intermine-bio package into intermine-ws-python package

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#12 13 comments 0 reactions 1 assignee Claimed by @mbasil09 View on GitHub
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Description

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

1. copy over init and iterators files
2. rename them something bio specific (I think we want a bio directory?)
3. write tutorial
4. test!

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