Fixed whitespace errors and re-updated pep8 compliance.

chipathlon/conf.py

@@ -20,16 +20,19 @@ 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"
+resources = {
+    "walltime": {
+        "namespace": "globus",
+        "key": "maxwalltime"
     },
-	      "memory" :  { "namespace" : "condor",
-                            "key"       : "request_memory"
+    "memory": {
+        "namespace": "condor",
+        "key": "request_memory"
     }
 }
 

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):
@@ -253,7 +254,7 @@ class Workflow(object):
                         # 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):
@@ -334,7 +335,7 @@ class Workflow(object):
                 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

@@ -92,10 +92,10 @@ class WorkflowJob(object):
             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)
+                        % (resource_type, self.jobname)
             except TypeError:
                 self.err += "Resource specification of type '%s' for '%s' is missing a value.\n" \
-                                                % (resource_type,self.jobname)
+                    % (resource_type, self.jobname)
             except KeyError:
                 pass
         return
@@ -136,7 +136,7 @@ class WorkflowJob(object):
             print self.err
         return None
 
-    def _add_job_resources(self,job):
+    def _add_job_resources(self, job):
         """
         Add the job's resources (memory, walltime, etc.) via Pegasus
         Profiles.
@@ -148,7 +148,7 @@ class WorkflowJob(object):
                 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)
+            job.profile(ns, key, resource_value)
 
     def _create_arg_list(self, input_files, output_files):
         """