ajout oncologie

create_html.py

@@ -125,7 +125,8 @@ for record in vcf_reader_SNP.fetch():
     try:
         for i in range(len(record.info["Pharmaco_Annot"])/12):
             try:
-                gene = repr(record.info["GENEINFO"])
+                gen = repr(record.info["GENEINFO"])
+		gene = gen[1:]
             except:
                 gene = "intron"
             alt = record.info["Pharmaco_Annot"][(i*12)+1].replace(")","").replace("'","").replace("-","")
@@ -141,7 +142,7 @@ for record in vcf_reader_SNP.fetch():
                 body= body.append(htmltag.P(htmltag.P2("pathologie: "+patho))+htmltag.P(htmltag.P2("molecule: "+molecule))+htmltag.P(htmltag.P2("gene: "+gene.encode('utf-8')))+htmltag.P(htmltag.P2("variant: "+repr(record.pos)+" "+repr(record.ref)+">"+repr(record.alts)+" "+repr(record.id)))+htmltag.P(htmltag.P2("base alternative: "+alt))+htmltag.P(htmltag.P2("niveau: "+level))+htmltag.P(htmltag.P2("phenotype: "+pheno)))
 		body= body.append(htmltag.P(htmltag.P2(htmltag.A(href = publi).append("publication: "+publi))))
             else :
-                body= body.append(htmltag.P("pathologie: "+patho)+htmltag.P("molecule: "+molecule)+htmltag.P("gene: "+gene.encode('utf-8')+type(gene))+htmltag.P("variant: "+repr(record.pos)+" "+repr(record.ref)+">"+repr(record.alts)+" "+repr(record.id))+htmltag.P("base alternative: "+alt)+htmltag.P("niveau: "+level)+htmltag.P(htmltag.P("phenotype: "+pheno)))
+                body= body.append(htmltag.P("pathologie: "+patho)+htmltag.P("molecule: "+molecule)+htmltag.P("gene: "+gene.encode('utf-8'))+htmltag.P("variant: "+repr(record.pos)+" "+repr(record.ref)+">"+repr(record.alts)+" "+repr(record.id))+htmltag.P("base alternative: "+alt)+htmltag.P("niveau: "+level)+htmltag.P(htmltag.P("phenotype: "+pheno)))
 		body= body.append(htmltag.P(htmltag.A(href = publi).append("publication: "+publi)))
             body= body.append(htmltag.P("#######################################################################"))
     except:

haplo_scan.sh

@@ -69,7 +69,7 @@ RES=${SORTIE}
 GL=/work/gad/shared/bin/HLAscan_v1.0/hla-ref-5gene/gene_list
 
 #Launch haplo_scan
-/work/gad/shared/bin/miniconda2/bin/python2.7 /work/gad/shared/bin/HLAscan_v1.0/hla-paper/haplo_scan_v4.0-sv.py $BAM $GL $RES
+/bin/python2.7 /work/gad/shared/bin/HLAscan_v1.0/hla-paper/haplo_scan_v4.0-sv.py $BAM $GL $RES
 
 hla_exitcode=$?
 echo "hla_scan exit code : $hla_exitcode"

pharmconfig_epilepsie.tsv

+HLAlist	/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
+pharmagkbase	/work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf
+pharmagktab	/work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv
+omim	/work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv
+header	/work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
+reference	/work/gad/shared/pipeline/hg19/index/hg19_essential.fa

pharmconfig_oncologie.tsv

+HLAlist	/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
+pharmagkbase	/work/gad/sv347413/epilepsie/Pipeline/pharmgkb_oncologie.vcf
+pharmagktab	/work/gad/sv347413/epilepsie/Pipeline/tableau_oncologie.tsv
+omim	/work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM_oncologie.tsv
+header	/work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
+reference	/work/gad/shared/pipeline/hg19/index/hg19_essential.fa