Merge pull request #202 from Ecogenomics/python3_dev

try/except clause for 3rd party software.

gtdbtk/VERSION

@@ -1,3 +1,5 @@
+1.0.1
+- Bugfix for 3rd party software versions. 
 1.0.0
 - Migrated to Python3.
 - check_install now does an exhaustive check of the reference data.

gtdbtk/external/fasttree.py

@@ -34,12 +34,15 @@ def __init__(self):
 
     def get_version(self):
         """ Get FastTree version. """
-        env = os.environ.copy()
-        args = ['FastTree']
-        proc = subprocess.Popen(args, stdout=subprocess.PIPE,
+        try:
+            env = os.environ.copy()
+            args = ['FastTree']
+            proc = subprocess.Popen(args, stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE, env=env, encoding='utf-8')
-        output, error = proc.communicate()
-        return error.split('\n')[0].split(' ')[4]
+            output, error = proc.communicate()
+            return error.split('\n')[0].split(' ')[4]
+        except:
+            return "(version unavailable)"
 
     def run(self, output_tree, tree_log, fasttree_log, prot_model, no_support, no_gamma, msa_file, cpus=1):
         """Run FastTree.

gtdbtk/external/hmm_aligner.py

@@ -63,15 +63,20 @@ def __init__(self,
 
     def get_version(self):
         """ get HMMER version."""
-        env = os.environ.copy()
-        proc = subprocess.Popen(['hmmalign', '-h'], stdout=subprocess.PIPE,
+        try:
+            env = os.environ.copy()
+            proc = subprocess.Popen(['hmmalign', '-h'], stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE, env=env, encoding='utf-8')
 
-        output, error = proc.communicate()
-        for line in output.split('\n'):
-            if line.startswith('# HMMER'):
-                version = line.split(';')[0].replace('# HMMER', '').strip()
-                return version
+            output, error = proc.communicate()
+            for line in output.split('\n'):
+                if line.startswith('# HMMER'):
+                    version = line.split(';')[0].replace('# HMMER', '').strip()
+                    return version
+            return "(version unavailable)"
+        except:
+            return "(version unavailable)"
+
 
     def align_marker_set(self, db_genome_ids, marker_set_id):
         """Threaded alignment using hmmalign for a given set of genomes.

gtdbtk/external/pplacer.py

@@ -103,12 +103,15 @@ def __init__(self):
         self.version = self._get_version()
 
     def _get_version(self):
-        env = os.environ.copy()
-        proc = subprocess.Popen(['pplacer', '--version'], stdout=subprocess.PIPE,
+        try:
+            env = os.environ.copy()
+            proc = subprocess.Popen(['pplacer', '--version'], stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE, env=env, encoding='utf-8')
 
-        output, error = proc.communicate()
-        return output.strip()
+            output, error = proc.communicate()
+            return output.strip()
+        except:
+            return "(version unavailable)"
 
     def run(self, cpus, model, ref_pkg, json_out, msa_file, pplacer_out,
             mmap_file=None):

gtdbtk/external/prodigal.py

@@ -56,13 +56,16 @@ def __init__(self,
         self.version = self._get_version()
 
     def _get_version(self):
-        env = os.environ.copy()
-        proc = subprocess.Popen(['prodigal', '-v'], stdout=subprocess.PIPE,
+        try:
+            env = os.environ.copy()
+            proc = subprocess.Popen(['prtrrodigal', '-v'], stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE, env=env, encoding='utf-8')
 
-        output, error = proc.communicate()
+            output, error = proc.communicate()
 
-        return error.split('\n')[1].split()[1].replace(':', '')
+            return error.split('\n')[1].split()[1].replace(':', '')
+        except:
+            return "(version unavailable)"
 
     def _run_prodigal(self, genome_id, fasta_path):
         """Run Prodigal.

gtdbtk/external/tigrfam_search.py

@@ -49,15 +49,19 @@ def __init__(self,
 
     def _get_version(self):
         """ get HMMER version."""
-        env = os.environ.copy()
-        proc = subprocess.Popen(['hmmsearch', '-h'], stdout=subprocess.PIPE,
+        try:
+            env = os.environ.copy()
+            proc = subprocess.Popen(['hmmsearch', '-h'], stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE, env=env, encoding='utf-8')
 
-        output, error = proc.communicate()
-        for line in output.split('\n'):
-            if line.startswith('# HMMER'):
-                version = line.split(';')[0].replace('# HMMER', '').strip()
-                return version
+            output, error = proc.communicate()
+            for line in output.split('\n'):
+                if line.startswith('# HMMER'):
+                    version = line.split(';')[0].replace('# HMMER', '').strip()
+                    return version
+            return "(version unavailable)"
+        except:
+            return "(version unavailable)"
 
     def _topHit(self, tigrfam_file):
         """Determine top hits to TIGRFAMs.