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import re
import sys
## generate the html page for the top genes
## put gene names and alias in a dictionary
#ncbi_gene_symb_syno_name_txid9606_absCnt_sorted_absCnt_sorted_absCnt_absCnt_sorted.txt
if (len(sys.argv) != 2):
print ("please provide the name of a sorted gene abstract count file")
sys.exit()
geneNames={}
with open (sys.argv[1],"r") as f:
for line in f:
(genes, count)=line.strip().split("\t")
gene=genes.split("|")
names=re.sub(r'^.*?\|', "", genes)
geneNames[gene[0]]=names.strip().replace("|", "; ")
out=str()
html=str()
with open("./topGeneAbstractCount.tab" ,"r") as gc:
cnt=0
for line in gc:
cnt+=1
line=re.sub(r'^\s+','',line)
print (line)
pmid_cnt, symb=line.strip().split()
out+= symb+"\t"+geneNames[symb]+"\n"
html+="<li><a href=\"/showTopGene?topGene="+symb+"\">"+symb+"</a> <span style=\"font-size:small; color:grey\">("+geneNames[symb]+")</span><br>\n"
if cnt==200:
break
with open("topGene_symb_alias.txt", "w+") as tg:
tg.write(out)
tg.close()
htmlout='''
{% extends "layout.html" %}
{% block content %}
<h3> Top addiction related genes </h3>
<br>
These genes are ranked by the number of PubMed abstracts that contain the name of the gene and one or more addiction related keyword.
<hr>
<ol>''' + html + '''
</ol>
{% endblock %}
'''
with open("./templates/topAddictionGene.html", "w+") as html_f:
html_f.write(htmlout)
html_f.close()
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