Updating report python code and removing vep step from workflow

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/annotation/new/generatereport.py b/annotation/new/generatereport.py
index c9bb5f1b7b0484592256bafbf923f6951929840d..6f39bb5bdb2f0c403bb66a349831e52a92304829 100644 (file)
--- a/annotation/new/generatereport.py
+++ b/annotation/new/generatereport.py
@@ -2,56 +2,75 @@ import numpy as np
 import scipy as scipy
 import pandas as pd
 import io
+import argparse
 
-pd.set_option("display.max_colwidth", 10000)
+def generatereport():
 
-filename = "reportdata.txt"
-samplename = "hu34D5B9_var-GS000015891-ASM"
-headfile = "head.html"
-tailfile = "tail.html"
+    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()
 
-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']="."
+    pd.set_option("display.max_colwidth", 10000)
 
-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'
+#    filename = "reportdata.txt"
+#    samplename = "hu34D5B9_var-GS000015891-ASM"
+#    headfile = "head.html"
+#    tailfile = "tail.html"
 
-#reportdata['URL'] =reportdata['Variant ID'].apply(lambda x: '<a href="www.ncbi.nlm.nih.gov/clinvar/variation/'+str(x)+'> Link </a>')
-reportdata['URL'] = '<a href="http://www.mywebsite.com/about.html">About</a>'
-reportdata.to_json('test.json',orient='records')
-str_io = io.StringIO()
+    filename = args.txtfilename
+    samplename = args.samplename
+    headfile = args.headfile
+    tailfile = args.tailfile
 
-reportdatasub = reportdata[["Variant ID", "Allele ID", "Clinical Significance","Disease Name", "Frequency EXAC", "Frequency 1000 Genomes Project","Zygosity","URL"]]
+    # 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']="."
 
-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')
+    # 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'
 
-html_str_encoded = html_str_encoded.replace('&lt;','<')
-html_str_encoded = html_str_encoded.replace('&gt;','>')
-html_str_encoded = html_str_encoded.replace('|','<br/>')
+    # creating url from variant ID
+    reportdata['URL'] = '<a href="http://www.mywebsite.com/about.html">About</a>'
+    reportdata.to_json('test.json',orient='records')
+    str_io = io.StringIO()
 
-html_file = open(headfile, 'r')
-source_code_head = html_file.read() 
-html_file.close()
+    # 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('&lt;','<')
+    html_str_encoded = html_str_encoded.replace('&gt;','>')
+    html_str_encoded = html_str_encoded.replace('|','<br/>')
 
-html_file = open(tailfile, 'r')
-source_code_tail = html_file.read()
-html_file.close()
+    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()
 
-total_html = source_code_head + html_str_encoded + source_code_tail
+    # 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()
 
-f = open(samplename+'.html','wb')
-
-f.write(total_html)
-f.close()
+if __name__ == '__main__':
+    generatereport()