diff structurefold/Iterative_mapping/seq_track.py @ 113:aedb21527abd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/structurefold/Iterative_mapping/seq_track.py	Tue Apr 14 14:09:42 2015 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+from read_file import *
+from Bio import SeqIO
+
+unmap_file = sys.argv[1]
+reads_file = sys.argv[2]
+result_file = sys.argv[3]
+tp = sys.argv[4]
+
+
+unmap = read_t_file(unmap_file);
+
+h = file(result_file, 'w')
+
+reads = SeqIO.parse(reads_file,tp)
+um = set()
+for i in range(0, len(unmap)):
+    id_r = unmap[i][0]
+    um.add(id_r)
+
+for read in reads:
+    if read.id in um:
+        h.write('>')
+        h.write(read.id)
+        h.write('\n')
+        h.write(read.seq.tostring())
+        h.write('\n')
+    
+
+
+h.close()
+
+
+
+