diff sanitize_snv.py @ 0:0e54da14f831 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sanitize_snv.py	Thu Feb 18 18:59:53 2021 +0000
@@ -0,0 +1,24 @@
+import sys
+
+handle = open(sys.argv[1], 'r')
+out = open(sys.argv[2], 'w')
+for line in handle:
+    if line[0] == '#':
+        out.write(line)
+        continue
+    linelist = line.split('\t')
+    refcol = linelist[0].split('chr')
+    infocol = linelist[7].split('INDEL')
+    if len(infocol) > 1:
+        continue
+    if len(refcol) > 1:
+        refcol = refcol[1]
+    else:
+        refcol = refcol[0]
+    if refcol not in ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10',
+                      '11', '12', '13', '14', '15', '16', '17', '18', '19',
+                      '20', '21', '22', 'X', 'Y']:
+        continue
+    else:
+        linelist[0] = refcol
+        out.write('\t'.join(linelist))