Merge pull request #35 from martinghunt/master

Allow gage to fail as long as we got the stats; v0.10.3

iva/common.py

@@ -2,7 +2,7 @@
 import os
 import sys
 import subprocess
-version = '0.10.2'
+version = '0.10.3'
 
 class abspathAction(argparse.Action):
     def __call__(self, parser, namespace, value, option_string):

iva/qc_external.py

@@ -78,13 +78,17 @@ def run_gage(reference, scaffolds, outdir, nucmer_minid=80, clean=True):
         '>', gage_out
         ]), file=f)
     fastaq.utils.close(f)
-    common.syscall('bash ' + gage_script)
+    common.syscall('bash ' + gage_script, allow_fail=True)
+    if not os.path.exists(gage_out):
+        raise Error('Error running GAGE\nbash ' + gage_script)
     stats = dummy_gage_stats()
     wanted_stats = set(gage_stats)
     f = fastaq.utils.open_file_read(gage_out)
+    got_all_stats = False
 
     for line in f:
         if line.startswith('Corrected Contig Stats'):
+            got_all_stats = True
             break
         elif ':' in line:
             a = line.rstrip().split(': ')
@@ -98,6 +102,9 @@ def run_gage(reference, scaffolds, outdir, nucmer_minid=80, clean=True):
                     stats[a[0]] = float(stat)
     fastaq.utils.close(f)
 
+    if not got_all_stats:
+        raise Error('Error running GAGE\nbash ' + gage_script)
+
     if clean:
         to_clean = [
             'contigs.fa.delta',

setup.py

@@ -7,7 +7,7 @@ def read(fname):
 
 setup(
     name='iva',
-    version='0.10.2',
+    version='0.10.3',
     description='Iterative Virus Assembler',
     long_description=read('README.md'),
     packages = find_packages(),