# HG changeset patch
# User davidvanzessen
# Date 1394544269 14400
# Node ID 191d0df65d28a8f79f37981736ce9e9185dbc238
# Parent  477cab9c32d13b9f27fccc2021e3d785c0048e6b
Uploaded

diff -r 477cab9c32d1 -r 191d0df65d28 imgtconvert.py
--- a/imgtconvert.py	Fri Mar 07 07:51:03 2014 -0500
+++ b/imgtconvert.py	Tue Mar 11 09:24:29 2014 -0400
@@ -1,5 +1,8 @@
 import pandas as pd
-#pd.options.mode.chained_assignment = None  # default='warn'
+try:
+	pd.options.mode.chained_assignment = None  # default='warn'
+except:
+	pass
 import re
 import argparse
 import os
@@ -122,6 +125,7 @@
 #jPattern = re.compile(r"IGHJ[1-6]") #human
 jPattern = re.compile(r"IGHJ[1-6]|TRBJ[12]-[1-7]") #mouse and human
 
+
 def filterGenes(s, pattern):
     if type(s) is not str:
         return "NA"
@@ -145,4 +149,4 @@
 outFrame["CDR3 Length DNA"] = outFrame["CDR3 Seq DNA"].map(str).map(len)
 safeLength = lambda x: len(x) if type(x) == str else 0
 outFrame = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top D Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows?
-outFrame.to_csv(outFile, sep="\t", index=False, index_label="index")
\ No newline at end of file
+outFrame.to_csv(outFile, sep="\t", index=False, index_label="index")