Ignoring of useless-object-inheritance now ignored as test as it is r…

…equired for py2 and py3 compatibility. Added the ability to test if the bam file contained paired end reads

mg_common/tool/bam_utils.py

@@ -40,7 +40,7 @@
 # ------------------------------------------------------------------------------
 
 # Object inheritance is required for py2 compatiblity
-class bamUtils(object):  # pylint: disable=invalid-name,useless-object-inheritance
+class bamUtils(object):  # pylint: disable=invalid-name
     """
     Tool for handling bam files
     """
@@ -61,6 +61,16 @@ def bam_count_reads(bam_file, aligned=False):
 
         return pysam.view("-c", bam_file).strip()  # pylint: disable=no-member
 
+    @staticmethod
+    def bam_paired_reads(bam_file):
+        """
+        Wrapper to test if a bam file contains paired end reads
+        """
+        paired_count = pysam.view("-c", "-f", "1", bam_file).strip()  # pylint: disable=no-member
+        if int(paired_count) > 0:
+            return True
+        return False
+
     @staticmethod
     def bam_sort(bam_file):
         """
@@ -359,7 +369,7 @@ def check_header(bam_file):
 
 
 # Object inheritance is required for py2 compatiblity
-class bamUtilsTask(object):  # pylint: disable=invalid-name,useless-object-inheritance
+class bamUtilsTask(object):  # pylint: disable=invalid-name
     """
     Wrappers so that the function above can be used as part of a @task within
     COMPSs avoiding the files being copied around the infrastructure too many
@@ -685,6 +695,25 @@ def bam_stats(self, bam_file):  # pylint: disable=no-self-use
         bam_handle = bamUtils()
         return bam_handle.bam_stats(bam_file)
 
+    @task(returns=bool, bam_file=FILE_IN)
+    def bam_paired_reads(self, bam_file):  # pylint: disable=no-self-use
+        """
+        Wrapper for the pysam SAMtools view function to identify if a bam file
+        contains paired end reads
+
+        Parameters
+        ----------
+        bam_file : str
+            Location of the bam file that is to be indexed
+
+        Returns
+        -------
+        bool
+            True if the bam file contains paired end reads
+        """
+        bam_handle = bamUtils()
+        return bam_handle.bam_stats(bam_file)
+
     @task(bam_file=FILE_IN)
     def check_header(self, bam_file):  # pylint: disable=no-self-use
         """

mg_common/tool/common.py

@@ -24,7 +24,7 @@
 
 
 # Object inheritance is required for py2 compatiblity
-class cd(object):  # pylint: disable=too-few-public-methods, invalid-name, useless-object-inheritance
+class cd(object):  # pylint: disable=too-few-public-methods, invalid-name
     """
     Context manager for changing the current working directory
     """
@@ -42,7 +42,7 @@ def __exit__(self, etype, value, traceback):
 
 
 # Object inheritance is required for py2 compatiblity
-class common(object):  # pylint: disable=too-few-public-methods, invalid-name, useless-object-inheritance
+class common(object):  # pylint: disable=too-few-public-methods, invalid-name
     """
     Common functions that can be used generically across tools and pipelines
     """

scripts/travis/pylint_harness.sh

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-disabled="--disable=similarities,invalid-name,too-many-statements,too-many-arguments,too-many-locals,too-few-public-methods,relative-import,no-self-use"
+disabled="--disable=similarities,invalid-name,too-many-statements,too-many-arguments,too-many-locals,too-few-public-methods,relative-import,no-self-use,useless-object-inheritance"
 
 pylint ${disabled} --rcfile pylintrc mg_common/ > output.err