import numpy as np
import scipy as scipy
import pandas as pd
import io
import argparse
def generatereport():
parser = argparse.ArgumentParser()
parser.add_argument('txtfilename', metavar='VCF2TXTFILENAME', help='text file of info to annotate')
parser.add_argument('samplename', metavar='SAMPLENAME', help='name of sample to use on report')
parser.add_argument('headfile', metavar='REPORTHEADHTML', help='head html for report')
parser.add_argument('tailfile', metavar='REPORTTAILHTML', help='tail html for report')
args = parser.parse_args()
pd.set_option("display.max_colwidth", 10000)
# filename = "reportdata.txt"
# samplename = "hu34D5B9_var-GS000015891-ASM"
# headfile = "head.html"
# tailfile = "tail.html"
filename = args.txtfilename
samplename = args.samplename
headfile = args.headfile
tailfile = args.tailfile
# reading data into dataframe
headerlist = ["Variant ID", "Chromosome", "Position", "Ref","Alt","Allele ID", "Clinical Significance","Disease Name","Frequency GO-ESP", "Frequency EXAC", "Frequency 1000 Genomes Project","GT"]
reportdata = pd.read_csv(filename,header=0,names=headerlist,sep='\t')
reportdata['Zygosity']="."
# defining zygosity
idxHOM1 = reportdata.GT=='1|1'
idxHOM2 = reportdata.GT=='1/1'
idxHET1 = reportdata.GT=='1|0'
idxHET2 = reportdata.GT=='1/0'
idxHET3 = reportdata.GT=='0|1'
idxHET4 = reportdata.GT=='0/1'
idxHOM = idxHOM1 | idxHOM2
idxHET = idxHET1 | idxHET2 | idxHET3 | idxHET4
reportdata.Zygosity[idxHOM]='HOM'
reportdata.Zygosity[idxHET]='HET'
# creating url from variant ID
clinvarURL = "https://www.ncbi.nlm.nih.gov/clinvar/variation/"
reportdata['URL'] = ' Link to ClinVar'
reportdata.to_json('test.json',orient='records')
str_io = io.StringIO()
# creating html table from dataframe
reportdatasub = reportdata[["Variant ID", "Allele ID", "Clinical Significance","Disease Name", "Frequency EXAC", "Frequency 1000 Genomes Project","Zygosity","URL"]]
reportdatasub.to_html(buf=str_io, classes='table table-bordered',index_names=False,index=False)
html_str = str_io.getvalue()
html_str_encoded = unicode(html_str).encode('utf8')
html_str_encoded = html_str_encoded.replace('<','<')
html_str_encoded = html_str_encoded.replace('>','>')
html_str_encoded = html_str_encoded.replace('|','
')
html_file = open(headfile, 'r')
source_code_head = html_file.read()
html_file.close()
html_file = open(tailfile, 'r')
source_code_tail = html_file.read()
html_file.close()
# combine html table with head and tail html for total report
total_html = source_code_head + html_str_encoded + source_code_tail
# write out report html
f = open(samplename+'.html','wb')
f.write(total_html)
f.close()
if __name__ == '__main__':
generatereport()