pep8 fixes

scripts/flatten_json.py

@@ -1,30 +1,32 @@
-import sys
+#!/usr/bin/env python
+
 import json
+import sys
 from collections import OrderedDict
 
-###
-### gene1_name gene1_id, gene2_name, gene2_id, type, pair, split, txlist
 
 def loadJSON(fn):
     with open(fn) as f:
-        JJ = json.load(f,object_pairs_hook=OrderedDict)
+        JJ = json.load(f, object_pairs_hook=OrderedDict)
     return JJ['genes']
 
-def outputGeneTable(fusions, outf, filters = None):
+
+def outputGeneTable(fusions, outf, filters=None):
     outf.write('\t'.join("geneA.name geneA.id geneB.name geneB.id paircount splitcount transcripts.list".split()))
     outf.write('\n')
     for gf in fusions:
         gAname = gf['geneA']['name']
-        gAid   = gf['geneA']['id']
+        gAid = gf['geneA']['id']
         gBname = gf['geneB']['name']
-        gBid   = gf['geneB']['id']
-        pairs  = str(gf['paircount'])
-        split  = str(gf['splitcount'])
+        gBid = gf['geneB']['id']
+        pairs = str(gf['paircount'])
+        split = str(gf['splitcount'])
         txp = [tp['fasta_record'] for tp in gf['transcripts']]
 
         outf.write('\t'.join([gAname, gAid, gBname, gBid, pairs, split, ';'.join(txp)]))
         outf.write('\n')
 
+
 def usage():
     print("Usage: python flatten_json.py fusion.out.json [genetable.txt]")
     print("")
@@ -41,9 +43,9 @@ def usage():
         fusions = loadJSON(infn)
         outf = sys.stdout
         if nargs == 3:
-            outf = open(sys.argv[2],'w')
+            outf = open(sys.argv[2], 'w')
 
-        outputGeneTable(fusions,outf)
+        outputGeneTable(fusions, outf)
 
         if outf != sys.stdout:
             outf.close()

scripts/get_fragment_length.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 import h5py
 import numpy as np
 import sys
@@ -20,7 +22,7 @@ def get_cumulative_dist(fn):
         print("       cutoff:      percentage cutoff to use (default .95)")
     else:
         fn = sys.argv[1]
-        if len(sys.argv) >=3:
+        if len(sys.argv) >= 3:
             cutoff = float(sys.argv[2])
             if cutoff <= 0 or cutoff >= 1.0:
                 cutoff = 0.95