Merge pull request #95 from fls-bioinformatics-core/ensure-all-classe…

…s-inherit-from-object

Update Python classes to ensure that they all explicitly subclass 'object'

ChIP-seq/make_macs2_xls.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     make_macs2_xls.py: Convert MACS output file to XLS(X) spreadsheet
-#     Copyright (C) University of Manchester 2013-2016 Peter Briggs, Ian Donaldson
+#     Copyright (C) University of Manchester 2013-2019 Peter Briggs, Ian Donaldson
 #
 ########################################################################
 #
@@ -48,13 +48,13 @@
 # Module metadata
 #######################################################################
 
-__version__ = '0.5.0'
+__version__ = '0.5.1'
 
 #######################################################################
 # Class definitions
 #######################################################################
 
-class MacsXLS:
+class MacsXLS(object):
     """Class for reading and manipulating XLS output from MACS
 
     Reads the XLS output file from the MACS peak caller and

NGS-general/manage_seqs.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     manage_seqs.py: Utility for handling sets of named sequences
-#     Copyright (C) University of Manchester 2014 Peter Briggs
+#     Copyright (C) University of Manchester 2014-2019 Peter Briggs
 #
 ########################################################################
 #
@@ -25,7 +25,7 @@
 # Module metadata
 #######################################################################
 
-__version__ = "0.0.2"
+__version__ = "0.0.3"
 
 #######################################################################
 # Import modules that this module depends on
@@ -40,7 +40,7 @@
 # Classes
 #######################################################################
 
-class SeqDb:
+class SeqDb(object):
     """Class for storing set of sequences with associated names
 
     SeqDb stores arbitrary sequence strings associated with

NGS-general/sam2soap.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     sam2soap.py: convert from SAM to SOAP format
-#     Copyright (C) University of Manchester 2012 Peter Briggs, Casey Bergman
+#     Copyright (C) University of Manchester 2012-2019 Peter Briggs, Casey Bergman
 #
 #######################################################################
 #
@@ -30,7 +30,7 @@
 # Class definitions
 #######################################################################
 
-class SAMBitwiseFlag:
+class SAMBitwiseFlag(object):
     """Class to decode bitwise flag from SAM file.
 
     Deconvolutes the decimal value of the bitwise flag from a
@@ -82,7 +82,7 @@ def __bitIsSet(self,data,bit):
         except IndexError:
             return False
 
-class SAMLine:
+class SAMLine(object):
     """Class to represent SAM alignment data line
 
     Decodes a SAM alignment data line and sets the class properties
@@ -155,7 +155,7 @@ def __init__(self,line=None):
             # Derived class properties
             self.bitwiseFlag = SAMBitwiseFlag(self.flag)
 
-class SOAPLine:
+class SOAPLine(object):
     """Class to represent SOAP file line
 
     The class has the following properties which can be set by

NGS-general/split_fasta.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     split_fasta.py: extract individual chromosome sequences from fasta file
-#     Copyright (C) University of Manchester 2013 Peter Briggs
+#     Copyright (C) University of Manchester 2013-2019 Peter Briggs
 #
 ########################################################################
 #
@@ -22,7 +22,7 @@
 # Module metadata
 #######################################################################
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 
 #######################################################################
 # Import modules
@@ -129,7 +129,7 @@ def next(self):
 import cStringIO
 
 # Test data
-class TestData:
+class TestData(object):
     """Set up example data to use in unit test classes
 
     """

RNA-seq/bowtie_mapping_stats.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     bowtie_mapping_stats.py: write Bowtie mapping stats to a spreadsheet
-#     Copyright (C) University of Manchester 2011-2014 Peter Briggs
+#     Copyright (C) University of Manchester 2011-2019 Peter Briggs
 #
 ########################################################################
 #
@@ -75,7 +75,7 @@
 # Module metadata
 #######################################################################
 
-__version__ = "1.1.5"
+__version__ = "1.1.6"
 
 #######################################################################
 # Import
@@ -113,7 +113,7 @@
 # Classes
 #######################################################################
 
-class BowtieMappingStats:
+class BowtieMappingStats(object):
     """Collect and output mapping statistics for multiple samples
 
     Read and store mapping stats from one or more samples from one
@@ -337,7 +337,7 @@ def tab_file(self,tab_file=None):
             open(tab_file,'w').write(txt)
         return txt
 
-class BowtieSample:
+class BowtieSample(object):
     """Store mapping statistics for a sample
 
     Simple holder for mapping statistics extracted from a bowtie

bcftbx/Experiment.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     Experiment.py: classes for defining SOLiD sequencing experiments
-#     Copyright (C) University of Manchester 2011-2013 Peter Briggs
+#     Copyright (C) University of Manchester 2011-2019 Peter Briggs
 #
 ########################################################################
 #
@@ -30,7 +30,7 @@
 # Class definitions
 #######################################################################
 
-class Experiment:
+class Experiment(object):
     """Class defining an experiment from a SOLiD run.
 
     An 'experiment' is a collection of related data.
@@ -89,7 +89,7 @@ def copy(self):
         expt_copy.library = self.library
         return expt_copy
 
-class ExperimentList:
+class ExperimentList(object):
     """Container for a collection of Experiments
 
     Experiments are created and added to the ExperimentList by calling
@@ -299,7 +299,7 @@ def __getitem__(self,key):
     def __len__(self):
         return len(self.experiments)
 
-class LinkNames:
+class LinkNames(object):
     """Class to construct names for links to primary data files
 
     The LinkNames class encodes a set of naming schemes that are used to

bcftbx/FASTQFile.py

@@ -1,5 +1,5 @@
 #     FASTQFile.py: read and manipulate FASTQ files and data
-#     Copyright (C) University of Manchester 2012-13 Peter Briggs
+#     Copyright (C) University of Manchester 2012-19 Peter Briggs
 #
 ########################################################################
 #
@@ -26,7 +26,7 @@
 
 """
 
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 CHUNKSIZE = 102400
 
@@ -144,7 +144,7 @@ def next(self):
         self._ip = ip
         return FastqRead(*read)
 
-class FastqRead:
+class FastqRead(object):
     """Class to store a FASTQ record with information about a read
 
     Provides the following properties for accessing the read data:
@@ -262,7 +262,7 @@ def __repr__(self):
     def __eq__(self,other):
         return (str(self) == str(other))
 
-class SequenceIdentifier:
+class SequenceIdentifier(object):
     """Class to store/manipulate sequence identifier information from a FASTQ record
 
     Provides access to the data items in the sequence identifier line of a FASTQ
@@ -386,7 +386,7 @@ def __repr__(self):
             # Return what was put in
             return self.__seqid
 
-class FastqAttributes:
+class FastqAttributes(object):
     """Class to provide access to gross attributes of a FASTQ file
 
     Given a FASTQ file (can be uncompressed or gzipped), enables

bcftbx/IlluminaData.py

@@ -44,7 +44,7 @@
 # Class definitions
 #######################################################################
 
-class IlluminaRun:
+class IlluminaRun(object):
     """Class for examining 'raw' Illumina data directory.
 
     Provides the following properties:
@@ -180,7 +180,7 @@ def cycles(self):
             return None
         return ncycles
 
-class IlluminaRunInfo:
+class IlluminaRunInfo(object):
     """Class for examining Illumina RunInfo.xml file
 
     Extracts basic information from a RunInfo.xml file:
@@ -244,7 +244,7 @@ def bases_mask(self):
                                 % read['is_indexed_read'])
         return ','.join(bases_mask)
 
-class IlluminaData:
+class IlluminaData(object):
     """Class for examining Illumina data post bcl-to-fastq conversion
 
     Provides the following attributes:
@@ -428,7 +428,7 @@ def get_project(self,name):
             if project.name == name: return project
         raise IlluminaDataError, "No matching project for '%s'" % name
 
-class IlluminaProject:
+class IlluminaProject(object):
     """Class for storing information on a 'project' within an Illumina run
 
     A project is a subset of fastq files from a run of an Illumina
@@ -615,7 +615,7 @@ def prettyPrintSamples(self):
         """
         return utils.pretty_print_names(self.samples)
 
-class IlluminaSample:
+class IlluminaSample(object):
     """Class for storing information on a 'sample' within an Illumina project
 
     A sample is a fastq file generated within an Illumina sequencer run.
@@ -734,7 +734,7 @@ def __repr__(self):
         i.e. the sample name."""
         return str(self.name)
 
-class SampleSheet:
+class SampleSheet(object):
     """
     Class for handling Illumina sample sheets
 
@@ -2313,7 +2313,7 @@ def set(self,package=None,paired_end=None,
         if force_sample_dir is not None:
             self._force_sample_dir = force_sample_dir
 
-class IlluminaFastq:
+class IlluminaFastq(object):
     """Class for extracting information about Fastq files
 
     Given the name of a Fastq file from CASAVA/Illumina platform, extract

bcftbx/Md5sum.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     Md5sum.py: classes and functions for md5 checksum operations
-#     Copyright (C) University of Manchester 2012-2014 Peter Briggs
+#     Copyright (C) University of Manchester 2012-2019 Peter Briggs
 #
 ########################################################################
 #
@@ -43,7 +43,7 @@ class methods for running MD5 checks across all files in a directory, and
 # Module metadata
 #######################################################################
 
-__version__ = "1.1.0"
+__version__ = "1.1.1"
 
 #######################################################################
 # Import modules that this module depends on
@@ -69,7 +69,7 @@ class methods for running MD5 checks across all files in a directory, and
 # Classes
 #######################################################################
 
-class Md5Checker:
+class Md5Checker(object):
     """Provides static methods for performing checks using MD5 sums
 
     The Md5Checker class is a collection of static methods that can
@@ -323,7 +323,7 @@ def verify_md5sums(self,filen=None,fp=None):
                 status = self.MD5_ERROR
             yield (f,status)
 
-class Md5CheckReporter:
+class Md5CheckReporter(object):
     """Provides a generic reporting class for Md5Checker methods
 
     Typical usage modes are either:

bcftbx/Pipeline.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     Pipeline.py: classes for running scripts iteratively
-#     Copyright (C) University of Manchester 2011 Peter Briggs
+#     Copyright (C) University of Manchester 2011-2019 Peter Briggs
 #
 ########################################################################
 #
@@ -47,7 +47,7 @@
 # Module metadata
 #######################################################################
 
-__version__ = "0.1.3"
+__version__ = "0.1.4"
 
 #######################################################################
 # Import modules that this module depends on
@@ -65,7 +65,7 @@
 #######################################################################
 
 # Job: container for a script run
-class Job:
+class Job(object):
     """Wrapper class for setting up, submitting and monitoring running scripts
 
     Set up a job by creating a Job instance specifying the name, working directory,
@@ -263,7 +263,7 @@ def runner(self):
         return self.__runner
 
 # PipelineRunner: class to set up and run multiple jobs
-class PipelineRunner:
+class PipelineRunner(object):
     """Class to run and manage multiple concurrent jobs.
 
     PipelineRunner enables multiple jobs to be queued via the 'queueJob' method. The