From 46c39f2d53c21b3bafb4c2263fafa76eeab8dab0 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 12 Jul 2010 19:13:32 +0000
Subject: [PATCH] Quick python scripts for going from genotype VCFs to
 site-only VCFs, and one to fix BC vcf files (which had "het" genotypes at
 non-variant sites)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3768 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/setFilterGenotypesToRef.py | 16 +++++++++++++
 python/vcfGenotypeToSites.py      | 38 +++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 python/setFilterGenotypesToRef.py
 create mode 100644 python/vcfGenotypeToSites.py

diff --git a/python/setFilterGenotypesToRef.py b/python/setFilterGenotypesToRef.py
new file mode 100644
index 000000000..e8944aa61
--- /dev/null
+++ b/python/setFilterGenotypesToRef.py
@@ -0,0 +1,16 @@
+import sys
+print("Fixing "+sys.argv[1]+" to "+sys.argv[2])
+bad_vcf = open(sys.argv[1])
+out_vcf = open(sys.argv[2],'w')
+
+for line in bad_vcf.readlines():
+    if ( line.startswith("#") ):
+        out_vcf.write(line)
+    else:
+        spline = line.strip().split("\t")
+        newspline = list()
+        for field in spline:
+            if ( field.find("pGeno") > -1 ):
+                field = "0/0:"+field.split(":",1)[1]
+            newspline.append(field)
+        out_vcf.write("\t".join(newspline)+"\n")
diff --git a/python/vcfGenotypeToSites.py b/python/vcfGenotypeToSites.py
new file mode 100644
index 000000000..203d51dfc
--- /dev/null
+++ b/python/vcfGenotypeToSites.py
@@ -0,0 +1,38 @@
+import sys
+genotype_vcf = open(sys.argv[1])
+sites_vcf = open(sys.argv[2],'w')
+
+sample_name = "ALL_HET"
+info = "."
+format = "GT"
+het = "0/1"
+use_fields = range(7)
+
+line_counter = 0
+print("Reading genotype file...")
+for line in genotype_vcf.readlines():
+    line_counter += 1
+    if ( line.startswith("#") and not line.startswith("#CHR") ):
+        sites_vcf.write(line)
+    elif ( line.startswith("#CHR") ):
+        sites_vcf.write("##source=vcfGenotypeToSites\n")
+        spline = line.strip().split("\t")
+        newfields = list()
+        for i in range(9):
+            newfields.append(spline[i])
+        newfields.append(sample_name)
+        sites_vcf.write("\t".join(newfields)+"\n")
+    else:
+        spline = line.strip().split("\t")
+        newfields = list()
+        for i in use_fields:
+            newfields.append(spline[i])
+        newfields.append(info)
+        newfields.append(format)
+        newfields.append(het)
+        sites_vcf.write("\t".join(newfields)+"\n")
+    if ( line_counter % 100000 == 0 ):
+        print("Converted: "+str(line_counter)+" lines")
+
+genotype_vcf.close()
+sites_vcf.close()