#!/usr/bin/env python2 import os os.environ[ 'HOME' ] = '/tmp/' import cgi, cgitb cgitb.enable() import pandas as pd import numpy as np import cgi, cgitb, urllib, jinja2, json #--- variation -------------- #SID='LOC_Os01g02860.1' httpfrom = cgi.FieldStorage() SID = httpfrom.getvalue('sID') if SID == None : SID='LOC_Os01g02860.1' variatyurl='http://sinin.kps.ku.ac.th/mutant/Varietyty.py?sID=' df=pd.read_csv('msu_call2018_imp_rename.tsv', sep="\t", header=0) chk_pheno=[x for x in open('phenonamelist.txt', 'r').read().split('\n')[:-1]] chk_gene=sorted(df.gene_id.unique().tolist()) vari='' haplo='' chro='' gstert='' gend='' gsnpid='' if SID in chk_gene: vari=df[df.gene_id == SID]['varity'].tolist() haplo=df[df.gene_id == SID]['haplotype'].tolist() chro=df[df.gene_id == SID]['chr'].tolist()[0] gstert=df[df.gene_id == SID]['gene_start'].tolist()[0] gend=df[df.gene_id == SID]['gene_end'].tolist()[0] gsnpid=df[df.gene_id == SID]['snpid'].tolist()[0] #---------------------------- def name2link(names, urllink, chk_list): outpu=names+', ' #pp='' if names in chk_list: outpu=''+names+', ' return outpu #---------------------------- valink=[] for x in vari: x=sorted(set(x.split(','))) tmplink=[name2link(x,variatyurl, chk_pheno) for x in x] valink.append(tmplink) tza=zip(haplo,valink) #-------------------------------------------- print """ Haplotype in gene """ print " \n " set1=""" """ set2=""" """ set3="""
Haplotype Variaty
Haplotype Variaty
""" set4="""

Search for Haplotype Variation by Gene:

Input gene ID from MSU annotation (e.g., LOC_Os01g08570.1, LOC_Os02g17460.1)

""" set5="""
""" print set4 print set5 print '
' if SID in chk_gene: print "

Search Results:

" print "

Haplotype in gene " +SID+ "

" print "
" print "
" print "" print "" print "" print "" print "" print "" print "" print "
Gene ID"+SID+"
Charomosome"+str(chro)+"
Gene start"+str(gstert)+"
gene end"+str(gend)+"
Haplotype"+','.join(haplo)+"
SNP ID"+gsnpid+"
" print "
" print set1 print "

" print "

Table of variaty in haplotype on gene " +SID+ "

" print "
" print set2 for x in tza: print ""+x[0]+''+''.join(x[1])+" " print set3 print "
" print "
" else : print "

No haplotype on gene " +SID+ " in this mutant population.

" print " \n "