--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flip_deletions.py	Mon Jan 23 10:05:02 2017 -0500
@@ -0,0 +1,37 @@
+#! /usr/bin/python
+
+from argparse import ArgumentParser
+import sys
+
+parser = ArgumentParser(description='Invert the TE deletion calls to give a consistent data format between TE insertions and deletions')
+parser.add_argument('-s', '--samples', help='list of all sample names', nargs="+", required=True)
+parser.add_argument('-d', '--deletions', help='merged TEPID deletions', required=True)
+parser.add_argument('-r', '--reference', help='reference sample name, eg Col-0', required=True)
+parser.add_argument('-o', '--output', help='output file name', required=True)
+options = parser.parse_args()
+
+
+def filter_del(options):
+    with open(options.deletions, 'r') as dels, open(options.output, 'w+') as outfile:
+        sample_names = options.samples
+        for line in dels:
+            line = line.strip().split('\t')
+            accessions = line[5]
+            sys.stderr.write(accessions)
+            sys.stderr.write(",".join(sample_names))
+            accessions = accessions.split(',')
+            coords = line[:4]
+            temp = [options.reference]
+            te = line[4]
+            for sample in sample_names:
+                if sample not in accessions:
+                    temp.append(sample)
+                else:
+                    pass
+            coords.pop(3)  # remove strand
+            info = '\t'.join(coords) + '\t' + te + '\t' + ','.join(temp) + '\n'
+            outfile.write(info)
+
+
+if __name__ == "__main__":
+    filter_del(options)