ajout profondeur et CNV

create_html_v2.py

 import sys
-
+import subprocess
 from pyexcel_ods import *
 from pysam import VariantFile
 import htmltag
@@ -57,6 +57,7 @@ for record in vcf_reader_CNV.fetch():
     for elm in record.alts:
         if elm == "<DEL>":
             ListeM = []
+            ListeD = []
             body= body.append(htmltag.P("Deletion detectee par xHMM sur le gene "+record.info["GENE"]))
             for i in range(len(data["hg19"])-1):
                 if not data["hg19"][i]:
@@ -68,6 +69,26 @@ for record in vcf_reader_CNV.fetch():
                                 ListeM.append(data["hg19"][i][0])
             for Mol in ListeM:
                 body= body.append(htmltag.P("######Gene ayant une relation avec :"+Mol))
+            depth_ave = 0.0
+            pos_len = 0
+            depth_new = 0
+            p = subprocess.Popen(["samtools", 'depth', BAM_FILE, '-r', record.chrom + ':' + str(record.pos) + '-'\
+            + str(record.stop)], stdout = subprocess.PIPE)
+            for line in p.stdout.readlines():
+                item = line.split()
+                if len(item) == 3:
+                    ListeD.append(item[2])
+                    for elm in ListeD:
+                        depth_new = depth_new + int(elm)
+                    depth_ave = depth_ave + float(item[2])
+                    pos_len = pos_len + (int(record.stop) - int(record.pos) + 1)
+            depth_ave = depth_new/float(pos_len)
+            if depth_ave > 40:
+                body= body.append(htmltag.P("######Detecte heterozygote, profondeur moyenne :"+depth_ave))
+            if depth_ave < 10:
+                body= body.append(htmltag.P("######Detecte  homozygote, profondeur moyenne :"+depth_ave))
+            else:
+                body= body.append(htmltag.P("######Detecte probablement heterozygote, profondeur moyenne :"+depth_ave))
         if elm == "<DUP>":
 	    ListeM = []
             body= body.append(htmltag.P("Duplication detectee par xHMM sur le gene "+record.info["GENE"]))