Add basic test of mainer_short.

lib/cryptosite/mainer_short.py

@@ -4,12 +4,12 @@
 
 from __future__ import print_function, absolute_import
 import sys
-from cryptosite.cleaning import *
-from cryptosite.seq_conservation import *
-from cryptosite.hyd_chr_sse import *
-from cryptosite.bmi_feature_parser import *
-from cryptosite.res_parser_bmi import *
-from cryptosite.patch_mapper import *
+import cryptosite.cleaning
+import cryptosite.seq_conservation
+import cryptosite.hyd_chr_sse
+import cryptosite.bmi_feature_parser
+import cryptosite.res_parser_bmi
+import cryptosite.patch_mapper
 import os
 import glob
 
@@ -58,7 +58,7 @@ def main():
     output = open('input.seq','w')
     querySeqs = {}
     for chain in chains:
-        querySeq = get_pdb_seq(pdb+'.pdb', chain)
+        querySeq = cryptosite.cleaning.get_pdb_seq(pdb+'.pdb', chain)
         querySeqs[chain] = querySeq
         output.write('>'+chain+'\n'+querySeq+'\n')
     output.close()
@@ -82,7 +82,8 @@ def main():
         sbjctSeq = querySeq
 
         # --- refine the structure (Modeller)
-        strcsq, seqsq = muscleAlign(querySeq, sbjctSeq, pdb, chain)
+        strcsq, seqsq = cryptosite.cleaning.muscleAlign(querySeq, sbjctSeq,
+                                                        pdb, chain)
         SubjectSeqList[chain] = seqsq
         QuerySeqList[chain] = strcsq
 
@@ -93,11 +94,10 @@ def main():
         output = open('test.seq','w')
         output.write('>%s%sq\n' % (pdb, chain) + sbjctSeq)
         output.close()
-        run_blast(pdb+chain)
-
-        parse_blast(pdb+chain+'.blast', pdb+chain, sbjctSeq)
-
+        cryptosite.seq_conservation.run_blast(pdb+chain)
 
+        cryptosite.seq_conservation.parse_blast(pdb+chain+'.blast', pdb+chain,
+                                                sbjctSeq)
 
     # --- change ali to pir
     out = open('alignment.pir','w')
@@ -122,7 +122,7 @@ def main():
     print(PDBChainOrder)
     print(ChainLenghts)
 
-    build_model(pdb, PDBChainOrder)
+    cryptosite.cleaning.build_model(pdb, PDBChainOrder)
 
     # --- Map SeqConservation to new residue numbering calculate HydChrSSE
 
@@ -143,19 +143,20 @@ def main():
         L+=len(SubjectSeqList[chain])
         seqdat.close()
         # -- hydrophobicity, charge, SSEs
-        HydChrSSE(pdb+'_mdl', mchains[PDBChainOrder.index(chain)])
+        cryptosite.hyd_chr_sse.HydChrSSE(pdb+'_mdl',
+                                         mchains[PDBChainOrder.index(chain)])
 
 
     # --- calculate PatchMap feature
-    patchmap_feature(pdb+'_mdl')
+    cryptosite.patch_mapper.patchmap_feature(pdb+'_mdl')
 
 
     # --- gather residue-based BMI features
-    gather_features(pdb+'_mdl',mchains)
+    cryptosite.bmi_feature_parser.gather_features(pdb+'_mdl',mchains)
 
 
     #for chain in PDBChainOrder:
-    res_parser(pdb+'_mdl')
+    cryptosite.res_parser_bmi.res_parser(pdb+'_mdl')
 
 
     # --- prepare AllosMod file

test/test_mainer.py

@@ -0,0 +1,69 @@
+import unittest
+import utils
+import os
+import sys
+import re
+import subprocess
+import shutil
+
+TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+utils.set_search_paths(TOPDIR)
+import cryptosite.mainer_short
+
+# Simply copy pre-built outputs at each step, rather than running BLAST,
+# fpocket, etc. (these are tested elsewhere)
+def mock_muscle_align(query, sbjct, pdb, chain):
+    return ('YVTEPCI', 'YVTEPCI')
+
+def mock_run_blast(pdbchain):
+    pass
+
+def mock_parse_blast(infile, pdbchain, seq):
+    shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdlA.sqc'),
+                'XXXA.sqc')
+
+def mock_build_model(pdb, chains):
+    shutil.copy('XXX.pdb', 'XXX_mdl.pdb')
+
+def mock_HydChrSSE(pdb, chain):
+    shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdlA.hcs'), '.')
+
+def mock_patchmap_feature(pdb):
+    shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdl.pdb.ptm'), '.')
+
+def mock_gather_features(pdb, chain_order):
+    shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdlA.feat'), '.')
+
+def mock_res_parser(fil):
+    shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdl.bmiftr'), '.')
+
+class Tests(unittest.TestCase):
+    def test_main(self):
+        """Test of complete run of mainer"""
+        with utils.temporary_working_directory() as tmpdir:
+            shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'),
+                        'input.pdb')
+            with open('param.txt', 'w') as fh:
+                fh.write("dummy\ndummy\nA\n")
+            with utils.mocked_objects(
+                    [(cryptosite.cleaning, 'muscleAlign', mock_muscle_align),
+                     (cryptosite.seq_conservation, 'run_blast', mock_run_blast),
+                     (cryptosite.seq_conservation, 'parse_blast',
+                      mock_parse_blast),
+                     (cryptosite.cleaning, 'build_model', mock_build_model),
+                     (cryptosite.hyd_chr_sse, 'HydChrSSE', mock_HydChrSSE),
+                     (cryptosite.patch_mapper, 'patchmap_feature',
+                      mock_patchmap_feature),
+                     (cryptosite.bmi_feature_parser, 'gather_features',
+                      mock_gather_features),
+                     (cryptosite.res_parser_bmi, 'res_parser',
+                      mock_res_parser)]):
+                cryptosite.mainer_short.main()
+            # Verify that AllosMod inputs were created
+            os.unlink('XXX/align.ali')
+            os.unlink('XXX/XXX.pdb')
+            os.unlink('XXX/input.dat')
+            os.unlink('XXX/list')
+
+if __name__ == '__main__':
+    unittest.main()

test/utils.py

@@ -53,6 +53,18 @@ def mocked_object(parent, objname, replacement):
     yield
     setattr(parent, objname, oldobj)
 
+@contextlib.contextmanager
+def mocked_objects(objs):
+    """Like mocked_object() but for a list of such tuples."""
+    oldobjs = []
+    for parent, objname, replacement in objs:
+        oldobjs.append(getattr(parent, objname))
+        setattr(parent, objname, replacement)
+    yield
+    for obj, oldobj in zip(objs, oldobjs):
+        parent, objname, replacement = obj
+        setattr(parent, objname, oldobj)
+
 if 'coverage' in sys.modules:
     import atexit
     # Collect coverage information from subprocesses