Merge pull request #75 from smirarab/bugfix

Bugfix

CHANGELOG.md

@@ -1,3 +1,5 @@
+* Version 4.3.10:
+     * fix issue #70 a bug when hmmsearch fake jobs where not piped
 * Version 4.3.9:
      * fix info file path in `run_sepp.sh` script
 * Version 4.3.7:

sepp/__init__.py

@@ -23,7 +23,7 @@
 
 __all__ = ["alignment", "shortreadalignment", "taxonneighbourfinder",
            "tools", "problem"]
-version = "4.3.9"
+version = "4.3.10"
 _DEBUG = ("SEPP_DEBUG" in os.environ) and \
     (os.environ["SEPP_DEBUG"].lower() == "true")
 

sepp/jobs.py

@@ -435,25 +435,28 @@ def read_results(self):
            Reads the search output file and returns a dictionary that contains
            the e-values of the searched fragments
         '''
-        if self.fake_run:
-            return {}
-        if self.pipe:
-            outfile = (self.stdoutdata.split("\n"))
-            return self.read_results_from_temp(outfile)
-        else:
-            assert os.path.exists(self.outfile)
-            assert os.stat(self.outfile)[stat.ST_SIZE] != 0
-            if self.results_on_temp:
+        if self.results_on_temp:
+            if self.fake_run:
+                res = {}
+            else:
+                assert os.path.exists(self.outfile)
+                assert os.stat(self.outfile)[stat.ST_SIZE] != 0
                 with open(self.outfile, 'r') as outfile:
                     res = self.read_results_from_temp(outfile)
-                with open(self.outfile, 'w') as target:
-                    target.write(str(res))
-                return self.outfile
+            with open(self.outfile, 'w') as target:
+                target.write(str(res))
+            return self.outfile
+        else:
+            if self.fake_run:
+                res = {}
+            elif self.pipe:
+                outfile = self.stdoutdata.split("\n")
+                res = self.read_results_from_temp(outfile)
             else:
                 outfile = open(self.outfile, 'r')
                 res = self.read_results_from_temp(outfile)
                 outfile.close()
-                return res
+            return res
 
         # Group 1 (e-value) 2 (bitscore) and 9 (taxon name) contain the
         # relevant information, other ones can be ignored unless we plan to

setup.py

@@ -30,7 +30,7 @@
 from distutils.spawn import find_executable
 
 use_setuptools(version="0.6.24")
-version = "4.3.9"
+version = "4.3.10"
 
 
 def get_tools_dir(where):

test/unittest/data/configs/test2.config

@@ -1,5 +1,5 @@
 [commandline]
-placementSize = 10
+placementSize = 40
 #alignment = data/simulated/test.small.fas
 #raxml = data/simulated/test.small.fas
 

test/unittest/data/q2-fragment-insertion/input_fragments_tiny.fasta

@@ -0,0 +1,2 @@
+>testseqa
+TACGTAGGATGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGGACTGTAAGTTGGATGTGAAATACCGTGGCTTAACCACGGAACTGCATCCAAAACTGTAGTTCTTGAGTG

test/unittest/testSepp.py

@@ -80,6 +80,21 @@ def test_seqnames_whitespaces(self):
             self.x.run()
         self.assertTrue(self.x.results is None)
 
+    def test_fake_jobs(self):
+        self.x.options.fragment_file = open(
+            get_data_path(
+                "q2-fragment-insertion/input_fragments_tiny.fasta"), "r")
+        self.x.run()
+        self.assertTrue(self.x.results is not None)
+
+    def test_notpiped_jobs(self):
+        sepp.config.options().hmmsearch.piped = "False"
+        self.x.options.fragment_file = open(
+            get_data_path(
+                "q2-fragment-insertion/input_fragments_tiny.fasta"), "r")
+        self.x.run()
+        self.assertTrue(self.x.results is not None)
+
 
 if __name__ == "__main__":
     unittest.main()