Technical development

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CGI Extravaganza! pulling categories from mediawiki(SNPedia)

  • local cgi with Fako & Natasha (feb,15th). From the terminal (local host), this python script pulls categories (default on 10) from SNPedia.
#!/usr/bin/python

import json, urllib2

search = u'Rs1001179' # quotes are string.
url = u'http://www.snpedia.com/api.php?action=query&format=json&redirects=true&generator=categories&titles=' + search
request = urllib2.Request(url)  
response = urllib2.urlopen(request)
result = response.read() 

f = json.loads(result)
print type(f)
g = json.dumps(f) # dump makes back into a string
print type(g)

for page in f['query']['pages'].itervalues():
        print page['title']

-Meaning that rsid number Rs1001179 is found in 10 categories in following results (terminal):

<type 'dict'>
<type 'str'>
Category:On chip Illumina Human 1M
Category:SNPs on chromosome 11
Category:In dbSNP
Category:Is a snp
Category:On chip 23andMe v3
Category:On chip HumanOmni1Quad
Category:On chip 23andMe v2
Category:Has population
Category:On chip 23andMe v1
Category:Has genotype



  • Server cgi with Michael (evening of feb,15th), viewed in browser

-first connect to the pzwart3 server in terminal:

sshfs awu@pzwart3.wdka.hro.nl:public_html mnt

-in index.html i define the parameters:

hello <br /><br />
my name is amy yeah

<p style="background: #ea9010; ">'rs10196796', '2', '229507242', 'TT'</p>

<div style="float: left; width: 20px; height: 20px; background: #ea9010; margin: 1px"></div>
<div style="float: left; width: 20px; height: 20px; background: #ea9010; margin: 1px"></div>
<div style="float: left; width: 20px; height: 20px; background: #eaffaa; margin: 1px"></div>
<div style="float: left; width: 20px; height: 20px; background: #ea3333; margin: 1px"></div>

<!-- http://pzwart3.wdka.hro.nl/~awu/ -->

visualisation: (note that url is: file:///home/socsoc/mnt/index.html) Indexhtml.png


-and use python as a 'motor' or 'conveyor belt' to mass produce the result:

#!/usr/bin/env python
#-*- coding:utf-8 -*-
import cgitb; cgitb.enable() 

print "Content-Type: text/html; charset=utf-8"     # HTML is following
print 

f = open ('wood.txt')

data = []
for line in f:
    if not line.startswith ('#'):
        d = line.strip().split()
        if len(d) == 4:
            data.append(d)

colors = {
    'TT': '#ea9010',
    'CT': '#FF0000'
}
for (rsid, chromosome, position, genotype) in data:
    print """<span style="width: 20px; background: """,
    print colors.get(genotype, 'black'),
    print """; margin: 1px">""",
    #print "&nbsp;",
    print genotype,
    print "</span>"
    print

visualisation: (note that url is: http://pzwart3.wdka.hro.nl/~awu/cgi-bin/genome.cgi) Genomecgi.png