from python2 to python3 > ok from command line

src/jflow/__init__.py

@@ -30,7 +30,7 @@ jflowconf = JFlowConfigReader()
 # if log file directory does not exist, create it
 log_directory = os.path.dirname(jflowconf.get_log_file_path())
 if not os.path.isdir(log_directory):
-    os.makedirs(log_directory, 0751)
+    os.makedirs(log_directory, 0o751)
     
 logging.basicConfig(level=logging.DEBUG,
                     format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',

src/jflow/abstraction.py

@@ -90,7 +90,7 @@ class MultiMap(Abstraction):
                 else:
                     iteration_inputs.append(inputs[iter])
                     
-                input_pattern = self._longestCommonSubstr(map(os.path.basename, map(str, iteration_inputs)))
+                input_pattern = self._longestCommonSubstr(list(map(os.path.basename, list(map(str, iteration_inputs)))))
                 
                 iteration_outputs = []
                 if isinstance(self.outputs, list):

src/jflow/component.py

@@ -54,14 +54,14 @@ class Component(object):
          @return : the list of outputs updated at the end of component execution.
         """
         dynamic_outputs = list()
-        for attribute_value in self.__dict__.values():
+        for attribute_value in list(self.__dict__.values()):
             if issubclass( attribute_value.__class__, DynamicOutput ):
                 dynamic_outputs.append( attribute_value )
         return dynamic_outputs
 
     def get_output_files(self):
         outputs = {}
-        for attribute_value in self.__dict__.values():
+        for attribute_value in list(self.__dict__.values()):
             if ( issubclass( attribute_value.__class__, DynamicOutput ) or
                  issubclass( attribute_value.__class__, OutputFileList) ):
                 for f in attribute_value:
@@ -130,7 +130,7 @@ class Component(object):
         self.params_order.append(name)
         self.__setattr__(name, new_param)
 
-    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
+    def add_parameter(self, name, help, default=None, type=str, choices=None, 
                       required=False, flag=None, group="default", display_name=None,   
                       cmd_format="", argpos=-1):
         new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
@@ -140,7 +140,7 @@ class Component(object):
         self.params_order.append(name)
         self.__setattr__(name, new_param)
 
-    def add_parameter_list(self, name, help, default=None, type=types.StringType, choices=None, 
+    def add_parameter_list(self, name, help, default=None, type=str, choices=None, 
                            required=False, flag=None, group="default", display_name=None,
                            cmd_format="", argpos=-1):
         if default == None: default = []
@@ -313,7 +313,7 @@ class Component(object):
     def execute(self):
         # first create the output directory
         if not os.path.isdir(self.output_directory):
-            os.makedirs(self.output_directory, 0751)
+            os.makedirs(self.output_directory, 0o751)
         # then run the component
         self.process()
     
@@ -422,7 +422,7 @@ class Component(object):
     def get_temporary_file(self, suffix=".txt"):
         # first check if tmp directory exists
         if not os.path.isdir(self.config_reader.get_tmp_directory()):
-            os.makedirs(self.config_reader.get_tmp_directory(), 0751)
+            os.makedirs(self.config_reader.get_tmp_directory(), 0o751)
         tempfile_name = os.path.basename(tempfile.NamedTemporaryFile(suffix=suffix).name)
         return os.path.join(self.config_reader.get_tmp_directory(), tempfile_name)
     

src/jflow/config_reader.py

@@ -20,7 +20,7 @@ import sys
 import inspect
 import logging
 
-from ConfigParser import ConfigParser, NoOptionError
+from configparser import RawConfigParser, NoOptionError
 
 from jflow.utils import which, display_error_message
 
@@ -34,12 +34,12 @@ class JFlowConfigReader(object):
     def __init__(self):
         """ 
         """
-        self.reader = ConfigParser()
+        self.reader = RawConfigParser()
         self.reader.read(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), self.CONFIG_FILE_PATH))
 
     def get_tmp_directory(self):
         if not os.path.isdir(self.reader.get("storage", "tmp_directory")):
-            os.makedirs(self.reader.get("storage", "tmp_directory"), 0751)
+            os.makedirs(self.reader.get("storage", "tmp_directory"), 0o751)
         return self.reader.get("storage", "tmp_directory")
         
     def get_work_directory(self):
@@ -48,7 +48,7 @@ class JFlowConfigReader(object):
     def get_exec(self, software):
         try:
             return self.reader.get("softwares", software)
-        except NoOptionError, e:
+        except NoOptionError:
             return None
 
     def get_resource(self, resource):
@@ -62,12 +62,12 @@ class JFlowConfigReader(object):
         try:
             return self.reader.get('storage', 'log_file')
         except :
-            raise Error("Failed when parsing the config file, no section logging found!")
+            raise NoOptionError("Failed when parsing the config file, no section logging found!")
         
     def get_makeflow_path(self):
         try:
             exec_path = self.reader.get("global", "makeflow")
-        except NoOptionError, e:
+        except NoOptionError:
             exec_path = None
         if exec_path is None: exec_path = "makeflow"
         if which(exec_path) == None:
@@ -79,7 +79,7 @@ class JFlowConfigReader(object):
         try:
             date_format = self.reader.get("global", "date_format")
         except:
-            raise Error("Failed when parsing the config file, no parameter date_format!")
+            raise NoOptionError("Failed when parsing the config file, no parameter date_format!")
         return date_format
 
     def get_batch(self):
@@ -88,7 +88,7 @@ class JFlowConfigReader(object):
             options = self.reader.get("global", "batch_options")
             limit_submission = self.reader.get("global", "limit_submission")
             return [type, options, limit_submission]
-        except NoOptionError, e:
+        except NoOptionError:
             return None
           
     def get_socket_options(self):

src/jflow/extparser.py

@@ -44,7 +44,7 @@ class ExternalParser(object):
         options = {'define_parameters'  : fn_define_parameters }
         
         if kwargs :
-            for key, val in kwargs.items() :
+            for key, val in list(kwargs.items()) :
                 options[key] = val
         
         ComponentType = type(component_name, (_SerializableNestedComponent,),options)

src/jflow/featureio.py

@@ -15,11 +15,11 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
             
-from featureiolib.bed import BEDReader
-from featureiolib.biom import Biom, BiomIO
-from featureiolib.gff3 import GFF3Record, GFF3IO
-from featureiolib.mpileup import MpileupReader
-from featureiolib.obo import OboReader
-from featureiolib.vcf import VCFReader
-from featureiolib.wego import WEGOReader
-from featureiolib.separatedvalue import SeparatedValueIO
\ No newline at end of file
+from .featureiolib.bed import BEDReader
+from .featureiolib.biom import Biom, BiomIO
+from .featureiolib.gff3 import GFF3Record, GFF3IO
+from .featureiolib.mpileup import MpileupReader
+from .featureiolib.obo import OboReader
+from .featureiolib.vcf import VCFReader
+from .featureiolib.wego import WEGOReader
+from .featureiolib.separatedvalue import SeparatedValueIO
\ No newline at end of file

src/jflow/seqio.py

@@ -28,11 +28,8 @@ import sys
 import struct
 import os
 import io
-if sys.version_info[0] < 3:
-    from itertools import izip as zip
-else:
-    basestring = str
-    from codecs import getreader, getwriter
+str = str
+from codecs import getreader, getwriter
 
 if sys.version_info < (2, 7):
     buffered_reader = lambda x: x
@@ -51,7 +48,7 @@ def xopen(filename, mode='r'):
     is used. If the filename is '-', standard output (mode 'w') or input
     (mode 'r') is returned.
     """
-    assert isinstance(filename, basestring)
+    assert isinstance(filename, str)
     if filename == '-':
         return sys.stdin if 'r' in mode else sys.stdout
     if filename.endswith('.gz'):
@@ -150,7 +147,7 @@ def SequenceReader(file, colorspace=False, fileformat=None):
     name = None
     if file == "-":
         file = sys.stdin
-    elif isinstance(file, basestring):
+    elif isinstance(file, str):
         name = file
     elif hasattr(file, "name"):
         name = file.name
@@ -197,7 +194,7 @@ class FastaReader(object):
         the file, but may obviously need a lot of memory.
         keep_linebreaks -- whether to keep the newline characters in the sequence
         """
-        if isinstance(file, basestring):
+        if isinstance(file, str):
             file = xopen(file, "r")
         self.fp = file
         self.wholefile = wholefile
@@ -277,7 +274,7 @@ class FastqReader(object):
         colorspace -- Usually (when this is False), there must be n characters in the sequence and
         n quality values. When this is True, there must be n+1 characters in the sequence and n quality values.
         """
-        if isinstance(file, basestring):
+        if isinstance(file, str):
             file = xopen(file, "r")
         self.fp = file
         self.colorspace = colorspace
@@ -333,7 +330,7 @@ class SFFReader(object):
         file is a filename or a file-like object.
         If file is a filename, then .gz files are supported.
         """
-        if isinstance(file, basestring):
+        if isinstance(file, str):
             file = xopen(file, "r")
         self.fp = file
         self.header_data = self.read_header(file)
@@ -631,7 +628,7 @@ class FastaQualReader(object):
         lengthdiff = 1 if self.colorspace else 0
         for fastaread, qualread in zip(self.fastareader, self.qualreader):
             if self.qual2ascii:
-                qualities = _quality_to_ascii(map(int, qualread.sequence.split()))
+                qualities = _quality_to_ascii(list(map(int, qualread.sequence.split())))
             elif self.splitqual:
                 qualities = qualread.sequence.split()
             else:
@@ -674,7 +671,7 @@ def writefasta(f, seqlist, linelength=None):
                 header = id
             f.write(header)
             f.write('\n')
-            for i in xrange(0, len(seq), linelength):
+            for i in range(0, len(seq), linelength):
                 f.write(seq[i:i+linelength])
                 f.write('\n')
     else:
@@ -694,7 +691,7 @@ def writequalities(f, seqlist, linelength=None):
     """
     if linelength is not None:
         for id, desc, seq, qual in seqlist:
-            if isinstance(qual, basestring):
+            if isinstance(qual, str):
                 qual = qual.split()
             f.write('>')
             header = id + ' ' + desc