EMBOSSwater.py

import urllib
import urllib2
from fasta import readFASTA
from collections import OrderedDict

url = 'http://www.ebi.ac.uk/Tools/services/rest/emboss_water/'
s=readFASTA("rosalind_laff.txt")
param_dict={
 'email':'jeremy.teitelbaum@uconn.edu',
 'title':'Local Alignment',
 'matrix': 'EBLOSUM62',
 'format':'markx3',
 'gapopen':15,
 'gapext':1,
}
param_dict['asequence']=s.values()[0]
param_dict['sid1']='A'
param_dict['bsequence']=s.values()[1]
param_dict['sid2']='B'
params = urllib.urlencode(param_dict)

response = urllib2.urlopen(url+'run/', params).read()
while urllib2.urlopen(url+'status/'+response).read()!="FINISHED":
    continue

answer=urllib2.urlopen(url+'resulttypes/'+response).read()

final=urllib2.urlopen(url+'result/'+response+'/out').read()
ls= [x for x in final.split('\n') if len(x)>0]
value,key="",""
s=OrderedDict({})
j=0
for x in ls: 
    if x[0] in ['#',';']:
        #print x
        continue  
    
    if x[0]==">":
        
        if key!="":
            s[key]=value
        key=x[1:].split()[0]+'-'+str(j)
        
        j=j+1
        value=""
    else:
        value=value+x.strip()
    
    s[key]=value

R=''
for x in s.values()[0]:
    if x!='-':
        R+=x
S=''
for x in s.values()[1]:
    if x!='-':
        S+=x
print R
print
print S
#print 
#print s.values()[1]