diff tools/protein_analysis/wolf_psort.py @ 19:f3ecd80850e2 draft

v0.2.9 Python style improvements

--- a/tools/protein_analysis/wolf_psort.py	Tue Sep 01 09:56:36 2015 -0400
+++ b/tools/protein_analysis/wolf_psort.py	Wed Feb 01 09:46:42 2017 -0500
@@ -35,7 +35,7 @@
 """
 import sys
 import os
-from seq_analysis_utils import sys_exit, split_fasta, run_jobs, thread_count
+from seq_analysis_utils import split_fasta, run_jobs, thread_count
 
 FASTA_CHUNK = 500
 exe = "runWolfPsortSummary"
@@ -56,44 +56,49 @@
 return_code = subprocess.call(args)
 os.chdir(saved_dir)
 sys.exit(return_code)
+
+For more details on this workaround, see:
+https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-December/023386.html
 """
 
 if len(sys.argv) != 5:
-    sys_exit("Require four arguments, organism, threads, input protein FASTA file & output tabular file")
+    sys.exit("Require four arguments, organism, threads, input protein FASTA file & output tabular file")
 
 organism = sys.argv[1]
 if organism not in ["animal", "plant", "fungi"]:
-    sys_exit("Organism argument %s is not one of animal, plant, fungi" % organism)
+    sys.exit("Organism argument %s is not one of animal, plant, fungi" % organism)
 
 num_threads = thread_count(sys.argv[2], default=4)
 fasta_file = sys.argv[3]
 tabular_file = sys.argv[4]
 
+
 def clean_tabular(raw_handle, out_handle):
     """Clean up WoLF PSORT output to make it tabular."""
     for line in raw_handle:
         if not line or line.startswith("#"):
             continue
-        name, data = line.rstrip("\r\n").split(None,1)
+        name, data = line.rstrip("\r\n").split(None, 1)
         for rank, comp_data in enumerate(data.split(",")):
             comp, score = comp_data.split()
-            out_handle.write("%s\t%s\t%s\t%i\n" \
-                             % (name, comp, score, rank+1))
+            out_handle.write("%s\t%s\t%s\t%i\n"
+                             % (name, comp, score, rank + 1))
 
 fasta_files = split_fasta(fasta_file, tabular_file, n=FASTA_CHUNK)
-temp_files = [f+".out" for f in fasta_files]
+temp_files = [f + ".out" for f in fasta_files]
 assert len(fasta_files) == len(temp_files)
 jobs = ["%s %s < %s > %s" % (exe, organism, fasta, temp)
         for (fasta, temp) in zip(fasta_files, temp_files)]
 assert len(fasta_files) == len(temp_files) == len(jobs)
 
+
 def clean_up(file_list):
     for f in file_list:
         if os.path.isfile(f):
             os.remove(f)
 
 if len(jobs) > 1 and num_threads > 1:
-    #A small "info" message for Galaxy to show the user.
+    # A small "info" message for Galaxy to show the user.
     print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
 results = run_jobs(jobs, num_threads)
 assert len(fasta_files) == len(temp_files) == len(jobs)
@@ -106,7 +111,7 @@
     if error_level or output.lower().startswith("error running"):
         clean_up(fasta_files)
         clean_up(temp_files)
-        sys_exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
+        sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
                  error_level)
 del results