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()