dotfiles

commit 833d1ce6afc1697722e81ab031450a20071ef7f9
parent 22260d4677378602d76e1ffa821d8f0a7588e85c
Author: Ed van Bruggen <edvb@uw.edu>
Date:   Sun, 27 Jan 2019 00:38:32 -0800

bin: Add aln2grishin

Diffstat:
bin/aln2grishin.py
 | 
42
++++++++++++++++++++++++++++++++++++++++++

1 file changed, 42 insertions(+), 0 deletions(-)
diff --git a/bin/aln2grishin.py b/bin/aln2grishin.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+"""
+Convert clustal alignment files to grishin for use in Rosetta protein
+simulations
+
+Author: Ed van Bruggen <edvb@uw.edu>
+"""
+
+import argparse
+from argparse import RawTextHelpFormatter
+
+parser = argparse.ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter)
+parser.add_argument('--file', type=str, required=True,
+                    help='input clustal alignment file')
+parser.add_argument('--target', metavar='POS', type=int, default=1,
+                    help='position of target protein (default: 1)')
+args = parser.parse_args()
+
+aln = open(args.file)
+proteins = []
+
+for i, line in enumerate(aln):
+    if i == 0 or line == '\n' or line[0] == ' ':
+        continue
+    words = line.split()
+    skip = 0
+    for protein in proteins:
+        if protein[0] == words[0]:
+            protein[1] += words[1]
+            skip = 1
+            continue
+    if not skip:
+        proteins.append([words[0], words[1]])
+
+target = proteins[args.target - 1]
+
+for protein in proteins:
+    if protein == target:
+        continue
+    grishin = open(target[0] + "_" + protein[0] + ".grishin", "w")
+    grishin.write("## %s %s_thread\n#\nscores from program: 0\n0 %s\n0 %s\n" %
+                  (target[0], protein[0], target[1], protein[1]))