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

[julie-sullivan]

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!

[yochannah]

I've added the hacktoberfest label to this issue. Note it's probably better to get started by trying some of the other hacktoberfest issues on this repo before you try this one.

[mbasil09]

@yochannah
I would like to try this.

[yochannah]

@mbasil09 Amazing - please go ahead! 😻

[mbasil09]

@yochannah
I think somewhere along the line the code in interminebio has been changed so much that it doesn't comply with the one in the main intermine repository. I tried changing it to python3, stil no luck.
I believe that the links that it tries to open have been updated, which raise errors.

I'll still try to pinpoint those errors and try to fix them.

[yochannah]

that sounds possible, and also like a really good reason to get it merged back into the main package. Thank you so much for tackling this! 😍

[mbasil09]

@yochannah
Any idea where the fasta or bed or gf3 files are stored.
The URLs used in interminebio are expired and give error404.

[yochannah]

@mbasil09 I can probably find them - where in interminebio are the broken links?

[mbasil09]

@yochannah
It tries to open this link (which doesn't exist):
http://www.flymine.org/query/service/check/query.fasta

it's in this file in the interminebio repository:
interminebio/iterators.py (Line 92)