A data retrieval workflow usingNCBI E-Utils + Python

Part II: Jinja2 / Flask

John PinneyTech talk Tue 19th Nov

My tasks

1. Produce a list of human genes that are associated withat least one resolved structure in PDBANDat least one genetic disorder in OMIM

2. Make an online table to display them

✓

Workflow for gene list

Python modules used in part 1

PyCogent Simple request handling for the main EUtils.pycogent.org

urllib2 General HTTP request handler.docs.python.org/2/library/urllib2.html

BeautifulSoup Amazingly easy to use object model for XML/HTML.www.crummy.com/software/BeautifulSoup/bs4/doc/

Some REST services need API keys

The OMIM server requires a license agreement but is free for academic use.They provide a personal API key which must be submitted with each HTTP request.

OMIM_APIKEY = 'E835870B16FBAF479E826FA5168CB2615EDA0F11'result = urllib2.urlopen( \

"http://api.europe.omim.org/api/entry?mimNumber=" + \ omimid + "&apiKey=" + OMIM_APIKEY \).read()

Throttling queries

Most bioinformatics web servers have limits on the number of queries that can be sent from the same IP address (per day / per second etc.)

They will ban you from accessing the site if you attempt too many requests.

This can have serious consequences (e.g. the whole institution being blocked from NCBI).

Throttling queries

To ensure compliance with usage limits, implement a simple throttle:

def omim_info(omimid):checktime('api.europe.omim.org')result = urllib2.urlopen(...

Throttling queries

import time

lastRequestTime = {}throttleDelay = {'eutils.ncbi.nlm.nih.gov':0.25, \

'api.europe.omim.org':0.5}

def checktime(host):if((host in lastRequestTime) and (time.time() - \

lastRequestTime[host] < throttleDelay[host])):

time.sleep(throttleDelay[host] - (time.time() - \ lastRequestTime[host]))

lastRequestTime[host] = time.time()

HTML templating

I need to produce an HTML table containing basic information about the genes I have collected.

The Jinja2 templating engine is an easy way to generate these kinds of documents.

I will use web services at NCBI and OMIM to assemble the information I need.

Jinja2

Using Jinja2 as an HTML templating engine, we need to split the work between 2 files:

a normal python script (in which I call the web services).an HTML template with embedded python commands.

Not all python functions are available within the template, so it makes sense to do as much work as possible within the script before passing the data over.

Jinja2 (script)

from jinja2 import Template

template = Template(file("gene_row_template.html").read())fout = open("gene_list.html",'w')...for g in sorted_genes:

fout.write( template.render(g=g,gene=gene_info(g),omim=[omim_info(x) for x in

omim_links(g)],struc=[struc_info(x) for x in

struc_links(g)])

)

(variables passed to template as kwargs)

Jinja2 (template)<tr>

<td><a href='http://www.ncbi.nlm.nih.gov/gene/?term={{g}}[uid]'>{{gene.find('Gene-ref_locus').text}}

</a></td><td>{{gene.find('Gene-ref_desc').text}}</td><td>{% for m in omim %}

<a href='http://omim.org/entry/{{m.mimNumber.text}}'>{{m.preferredTitle.text}}

</a><br>{% endfor %}</td>

<td>{% for s in struc -%}<a href='http://www.rcsb.org/pdb/explore/explore.do?

structureId={{s.find('Item',attrs={'Name':'PdbAcc'}).text}}'>{{s.find('Item',attrs={'Name':'PdbAcc'}).text}}

</a><br>{%- endfor %}</td>

</tr>

Jinja2 (template)<tr>

<td><a href='http://www.ncbi.nlm.nih.gov/gene/?term={{g}}[uid]'>{{gene.find('Gene-ref_locus').text}}

</a></td><td>{{gene.find('Gene-ref_desc').text}}</td><td>{% for m in omim %}

<a href='http://omim.org/entry/{{m.mimNumber.text}}'>{{m.preferredTitle.text}}

</a><br>{% endfor %}</td>

<td>{% for s in struc -%}<a href='http://www.rcsb.org/pdb/explore/explore.do?

structureId={{s.find('Item',attrs={'Name':'PdbAcc'}).text}}'>{{s.find('Item',attrs={'Name':'PdbAcc'}).text}}

</a><br>{%- endfor %}</td>

</tr>

{{ }} = print statement

{% %} = other command

I can access the methods of an object from within the template, so I can make use of all the nice BeautifulSoup shortcuts

Jinja2 (output)<tr>

<td><a href='http://www.ncbi.nlm.nih.gov/gene/?term=94[uid]'>ACVRL1

</a></td><td>activin A receptor type II-like 1</td><td>

<a href='http://omim.org/entry/600376'>TELANGIECTASIA, HEREDITARY HEMORRHAGIC, TYPE 2;

HHT2</a><br></td>

<td><a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=4FAO'>

4FAO</a><br><a

href='http://www.rcsb.org/pdb/explore/explore.do?structureId=3MY0'>3MY0

</a><br></td></tr>

Something more interactive

What if I need to produce a report on-the-fly?

Flask is a ‘micro’ web development framework for Python, which is useful for putting together a simple webserver.

For anything more substantial (e.g. if database queries are needed), consider using Django.

Flask uses Jinja2 as its template engine.

A simple webapp in Flaskfrom flask import Flask, request, render_template, Response

app = Flask(__name__)

@app.route('/report/')def report_handler():

gene = request.args.get('gene')if( gene == None):

return render_template('report_form.html', unfound=None)else:

return report_for_gene_name(gene)

if __name__ == '__main__':app.run(debug=True)

Summary

Some web services may be more fiddly than others to set up, especially if they involve

API keysRequest limits (requires throttling)

Combining web services with an HTML template (either offline or on-the-fly via a webserver) is an easy way to generate user-friendly reports.

Python modules used in part 2

Jinja2 An elegant and highly versatile templating engine.http://jinja.pocoo.org/

Flask Python ‘micro’ web development framework.http://flask.pocoo.org