---
layout: default
navsection: userguide
title: "Tutorial: Search PGP data by trait"
navorder: 20
---

h1. Tutorial: Search PGP data by trait

Here you will use the Python SDK to find public WGS data for people who have a certain medical condition.

h3. Prerequisites

* Log in to a VM "using SSH":ssh-access.html
* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable
* Put the API host name in your @ARVADOS_API_HOST@ environment variable
* Run the @python@ interactive shell.

If everything is set up correctly, you will be able to import the arvados SDK:

<pre>
import arvados
</pre>

...and display your account information:

<pre>
arvados.service.users().current().execute()
</pre>

h3. More prerequisites

<pre>
import re
import json
</pre>

h3. Find traits.

List traits containing the term "cancer":

<pre>
for t in filter(lambda t: re.search('cancer', t['name']),
                arvados.service.traits().list(limit=1000).execute()['items']):
  print t['uuid'], t['name']
</pre>

&darr;

<pre>
...
1h9kt-q1cn2-nu86efg57kzus5z Cervical cancer
1h9kt-q1cn2-0tl6w82sog50hlz Breast cancer
1h9kt-q1cn2-zkdn8edncaagqui Non-melanoma skin cancer
...
</pre>

We will use the "Non-melanoma skin cancer" trait with uuid @1h9kt-q1cn2-zkdn8edncaagqui@.

<pre>
trait_uuid = '1h9kt-q1cn2-zkdn8edncaagqui'
</pre>

h3. Find humans.

List humans who report this condition:

<pre>
trait_links = arvados.service.links().list(limit=1000,where=json.dumps({
    'link_class': 'human_trait',
    'tail_kind': 'arvados#human',
    'head_uuid': trait_uuid
  })).execute()['items']
</pre>

The "tail_uuid" attribute of each of these Links refers to a Human.

<pre>
map(lambda l: l['tail_uuid'], trait_links)
</pre>

&darr;

<pre>
[u'1h9kt-7a9it-c0uqa4kcdh29wdf', u'1h9kt-7a9it-x4tru6mn40hc6ah',
u'1h9kt-7a9it-yqb8m5s9cpy88i8', u'1h9kt-7a9it-46sm75w200ngwny',
u'1h9kt-7a9it-gx85a4tdkpzsg3w', u'1h9kt-7a9it-8cvlaa8909lgeo9',
u'1h9kt-7a9it-as37qum2pq8vizb', u'1h9kt-7a9it-14fph66z2baqxb9',
u'1h9kt-7a9it-e9zc7i4crmw3v69', u'1h9kt-7a9it-np7f35hlijlxdmt',
u'1h9kt-7a9it-j9hqyjwbvo9cojn', u'1h9kt-7a9it-lqxdtm1gynmsv13',
u'1h9kt-7a9it-zkhhxjfg2o22ywq', u'1h9kt-7a9it-nsjoxqd33lzldw9',
u'1h9kt-7a9it-ytect4smzcgd4kg', u'1h9kt-7a9it-y6tl353b3jc4tos',
u'1h9kt-7a9it-98f8qave4f8vbs5', u'1h9kt-7a9it-gd72sh15q0p4wq3',
u'1h9kt-7a9it-zlx25dscak94q9h', u'1h9kt-7a9it-8gronw4rbgmim01',
u'1h9kt-7a9it-wclfkjcb23tr5es', u'1h9kt-7a9it-rvp2qe7szfz4dy6',
u'1h9kt-7a9it-50iffhmpzsktwjm', u'1h9kt-7a9it-ul412id5y31a5o8',
u'1h9kt-7a9it-732kwkfzylmt4ik', u'1h9kt-7a9it-v9zqxegpblsbtai',
u'1h9kt-7a9it-kmaraqduit1v5wd', u'1h9kt-7a9it-t1nwtlo1hru5vvq',
u'1h9kt-7a9it-q3w6j9od4ibpoyl', u'1h9kt-7a9it-qz8vzkuuz97ezwv',
u'1h9kt-7a9it-t1v8sjz6dm9jmjf', u'1h9kt-7a9it-qe8wrbyvuqs5jew']
</pre>

h3. Find huIDs.

For now we don't need to look up the Human objects themselves. We just need to look up "identifier" links to find their huIDs:

<pre>
human_uuids = map(lambda l: l['tail_uuid'], trait_links)
huid_links = arvados.service.links().list(limit=1000,where=json.dumps({
    "link_class": "identifier",
    "head_uuid": human_uuids
  })).execute()['items']
map(lambda l: l['name'], huid_links)
</pre>

&darr;

<pre>
[u'huE2E371', u'huDF04CC', u'huD3A569', u'huD09534', u'huD09050', u'huB4883B',
 u'huB1FD55', u'huAB8707', u'hu9E356F', u'hu94040B', u'hu7A2F1D', u'hu7260DD',
 u'hu6C3F34', u'hu68F245', u'hu633787', u'hu602487', u'hu5E55F5', u'hu599905',
 u'hu5917F3', u'hu56B3B6', u'hu553620', u'hu474789', u'hu43860C', u'hu414115',
 u'hu397733', u'hu34A921', u'hu237A50', u'hu1BD549', u'hu174334', u'hu15402B',
 u'hu11603C', u'hu01024B']
</pre>

These huIDs let us find public profiles:

* "https://my.personalgenomes.org/profile/huE2E371":https://my.personalgenomes.org/profile/huE2E371
* "https://my.personalgenomes.org/profile/huDF04CC":https://my.personalgenomes.org/profile/huDF04CC
* ...