Fixed whitespace errors and re-updated pep8 compliance.

chipathlon/conf.py

@@ -20,17 +20,20 @@ file_extensions = {
     "bed": ["bed", "narrowPeak", "broadPeak"],
     "bwa_genome": ["amb", "ann", "bwt", "pac", "sa"],
     "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"],
-    "quality" : ["quality"]
+    "quality": ["quality"]
 }
 
 # list of resources that can be specified per job (step) in
 # the workflow and corresponding Pegasus profile info
-resources = { "walltime" :{ "namespace" : "globus",
-			    "key"	: "maxwalltime"
-			   },
-	      "memory" :  { "namespace" : "condor",
-                            "key"       : "request_memory"
-                           }
+resources = {
+    "walltime": {
+        "namespace": "globus",
+        "key": "maxwalltime"
+    },
+    "memory": {
+        "namespace": "condor",
+        "key": "request_memory"
+    }
 }
 
 # param keys

chipathlon/utils.py

@@ -47,6 +47,8 @@ def downloadFile(url, localpath, urltype="ftp://", retries=3, overwrite=True, ch
     else:
         print "File already exists, skipping download.\n"
     return
+
+
 # http://pythoncentral.io/how-to-check-if-a-string-is-a-number-in-python-including-unicode/
 def is_number(s):
     try:

chipathlon/workflow.py

@@ -15,6 +15,7 @@ import random
 from pprint import pprint
 from Pegasus.DAX3 import *
 
+
 class Workflow(object):
 
     def __init__(self, jobhome, run_file, param_file, config_file, host, username, password):
@@ -250,10 +251,10 @@ class Workflow(object):
                 if exp_name not in self.files and control_name not in self.files:
                     run["input_sets"].append(pair)
                     for f in pair:
-			# For each fastq, have Pegasus do the http fetching.
-			# Files are named EXPID_ACCESSION.fastq.gz
+                        # For each fastq, have Pegasus do the http fetching.
+                        # Files are named EXPID_ACCESSION.fastq.gz
                         output_name = "%s_%s.fastq.gz" % (run["experiment"], f["accession"])
-			self._add_file(output_name,"http://" + f["url"],"dummylocal")
+                        self._add_file(output_name, "http://" + f["url"], "dummylocal")
         return
 
     def _add_align(self):
@@ -307,7 +308,7 @@ class Workflow(object):
                 pegasus.catalog.site.file = %s/sites.xml
 
                 pegasus.condor.logs.symlink = false
-		pegasus.transfer.links=true
+                pegasus.transfer.links=true
                 pegasus.data.configuration = sharedfs
                 """ % (os.path.join(self.basepath, "input"),))
             wh.write(pegasusrc)
@@ -324,17 +325,17 @@ class Workflow(object):
                        <directory type="local-storage" path="%s">
                            <file-server operation="all" url="file://%s" />
                        </directory>""" % (
-					os.path.join(self.basepath, "work"),
-		                        os.path.join(self.basepath, "work"),
-					os.path.join(self.basepath, "output"),
-		                        os.path.join(self.basepath, "output")
-					)
+                    os.path.join(self.basepath, "work"),
+                    os.path.join(self.basepath, "work"),
+                    os.path.join(self.basepath, "output"),
+                    os.path.join(self.basepath, "output")
+                    )
             # NEED TO DETERMINE HOW TO READ IN THIS INFO
             for namespace in self.config["profile"]:
                 for key in self.config["profile"][namespace]:
                     sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, self.config["profile"][namespace][key])
 
-            sites +="""</site>
+            sites += """</site>
                    <site handle="dummylocal" arch="x86_64" os="LINUX">
                        <directory type="shared-scratch" path="%s">
                            <file-server operation="all" url="file://%s" />

chipathlon/workflow_job.py

@@ -44,7 +44,7 @@ class WorkflowJob(object):
             self._validate_input()
             if self.valid():
                 self._validate_arguments()
-		self._validate_resource_params()
+        self._validate_resource_params()
         return
 
     def _validate_input(self):
@@ -84,21 +84,21 @@ class WorkflowJob(object):
         return
 
     def _validate_resource_params(self):
-	"""
-	Validate memory/walltime values supplied in the params file
-	are present and numeric.
-	"""
-	for resource_type in chipathlon.conf.resources.keys():
-		try:
-			if not is_number(self.params[resource_type]):
-				self.err += "Resource specification of type '%s' for '%s' must be numeric.\n" \
-						% (resource_type,self.jobname)
-		except TypeError:
-				self.err += "Resource specification of type '%s' for '%s' is missing a value.\n" \
-                                                % (resource_type,self.jobname)
-		except KeyError:
-			pass
-	return
+        """
+        Validate memory/walltime values supplied in the params file
+        are present and numeric.
+        """
+        for resource_type in chipathlon.conf.resources.keys():
+            try:
+                if not is_number(self.params[resource_type]):
+                    self.err += "Resource specification of type '%s' for '%s' must be numeric.\n" \
+                        % (resource_type, self.jobname)
+            except TypeError:
+                self.err += "Resource specification of type '%s' for '%s' is missing a value.\n" \
+                    % (resource_type, self.jobname)
+            except KeyError:
+                pass
+        return
 
     def _check_files(self, input_files, additional_inputs, output_files):
         valid_files = True
@@ -130,25 +130,25 @@ class WorkflowJob(object):
             for f in output_files:
                 job.uses(f["file"], link=Link.OUTPUT, transfer=True)
             job.addArguments(*self._create_arg_list(input_files, output_files))
-	    self._add_job_resources(job)
+            self._add_job_resources(job)
             return job
         else:
             print self.err
         return None
 
-    def _add_job_resources(self,job):
-	"""
-	Add the job's resources (memory, walltime, etc.) via Pegasus
-	Profiles.
-	"""
-	for resource_type in chipathlon.conf.resources.keys():
-		try:
-			resource_value = self.params[resource_type]
-		except KeyError:
-			resource_value = self.base[self.jobname][resource_type]
-		ns = chipathlon.conf.resources[resource_type]["namespace"]
-		key = chipathlon.conf.resources[resource_type]["key"]
-		job.profile(ns,key,resource_value)
+    def _add_job_resources(self, job):
+        """
+        Add the job's resources (memory, walltime, etc.) via Pegasus
+        Profiles.
+        """
+        for resource_type in chipathlon.conf.resources.keys():
+            try:
+                resource_value = self.params[resource_type]
+            except KeyError:
+                resource_value = self.base[self.jobname][resource_type]
+            ns = chipathlon.conf.resources[resource_type]["namespace"]
+            key = chipathlon.conf.resources[resource_type]["key"]
+            job.profile(ns, key, resource_value)
 
     def _create_arg_list(self, input_files, output_files):
         """