diff extractHeaders.py @ 0:45cb248771d2 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractHeaders.py	Fri Oct 27 16:40:39 2017 -0400
@@ -0,0 +1,26 @@
+#!/usr/bin/python
+""" Extract headers from Fasta file and write the headers to a Tabular file """
+
+import sys
+
+def extractHeaders(fasta_file, tab_file):
+    
+    with open(tab_file, 'w') as out:
+        with open(fasta_file, 'r') as f:
+            lines = f.readlines()
+            for l in lines:
+                if '>' in l:
+                    l = l.split()
+                    name = l[0].replace('>', '').rstrip()
+                    desc = ''.join(l[1:]).rstrip()
+                    out.write(name + '\t' + desc + '\n')
+                
+
+
+def main(argv):
+    input_file = argv[1]
+    output_file = argv[2]
+    extractHeaders(input_file, output_file)
+
+if __name__ == "__main__":
+    main(sys.argv)