Merge branch 'dev'

HISTORY.md

@@ -1,3 +1,7 @@
+- 0.4.23
+
+* fix empty stats file [#61](https://github.com/miRTop/mirtop/issues/61) by @leontienvdbent
+
 - 0.4.22
 
 * fix when reads map halfway on to the edge

mirtop/command_line.py

@@ -24,7 +24,7 @@ def main(**kwargs):
                       kwargs['args'].print_debug)
     logger = mylog.getLogger(__name__)
     start = time.time()
-    logger.warning("This is devel-live changes")
+    #logger.warning("This is devel-live changes")
     if "gff" in kwargs:
         logger.info("Run annotation")
         reader(kwargs["args"])

mirtop/gff/stats.py

@@ -73,7 +73,7 @@ def _calc_stats(fn):
             cols = gff.columns
             attr = gff.attributes
             logger.debug("## STATS: attribute %s" % attr)
-            if ok.match(attr['Filter']):
+            if not ok.match(attr['Filter']):
                 continue
             if "-".join([attr['UID'], attr['Variant'], attr['Name']]) in seen:
                 continue

setup.py

@@ -3,7 +3,7 @@
 import os
 from setuptools import setup, find_packages
 
-version = '0.4.22'
+version = '0.4.23'
 
 url = 'http://github.com/mirtop/mirtop'
 

test/test_automated_analysis.py

@@ -307,20 +307,10 @@ def test_srnaseq_stats(self):
             print("")
             print(" ".join(clcode))
             subprocess.check_call(clcode)
-
-    @attr(complete=True)
-    @attr(cmd_stats=True)
-    @attr(cmd=True)
-    def test_srnaseq_stats(self):
-        """Run stats analysis
-        """
-        with make_workdir():
-            clcode = ["mirtop",
-                      "stats",
-                      "../../data/examples/gff/correct_file.gff"]
-            print("")
-            print(" ".join(clcode))
-            subprocess.check_call(clcode)
+            if not os.path.exists("test_out_mirs/mirtop_stats.txt"):
+                raise ValueError("File doesn't exist, something is wrong with stats cmd.")
+            if sum(1 for line in open('test_out_mirs/mirtop_stats.txt')) == 1:
+                raise ValueError("File is empty, something is wrong with stats cmd.")
 
     @attr(complete=True)
     @attr(cmd_merge=True)