Mercurial > repos > davidvanzessen > imgt_loader_igg

comparison imgtconvert.py @ 3:191d0df65d28 draft

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Uploaded
author davidvanzessen
date Tue, 11 Mar 2014 09:24:29 -0400
parents 477cab9c32d1
children 021d39f6bb0e
comparison
equal deleted inserted replaced
2:477cab9c32d1 3:191d0df65d28
1 import pandas as pd 1 import pandas as pd
2 #pd.options.mode.chained_assignment = None # default='warn' 2 try:
3 pd.options.mode.chained_assignment = None # default='warn'
4 except:
5 pass
3 import re 6 import re
4 import argparse 7 import argparse
5 import os 8 import os
6 9
7 def stop_err( msg, ret=1 ): 10 def stop_err( msg, ret=1 ):
120 123
121 #jPattern = re.compile(r"TRBJ[12]-[1-7]") #mouse 124 #jPattern = re.compile(r"TRBJ[12]-[1-7]") #mouse
122 #jPattern = re.compile(r"IGHJ[1-6]") #human 125 #jPattern = re.compile(r"IGHJ[1-6]") #human
123 jPattern = re.compile(r"IGHJ[1-6]|TRBJ[12]-[1-7]") #mouse and human 126 jPattern = re.compile(r"IGHJ[1-6]|TRBJ[12]-[1-7]") #mouse and human
124 127
128
125 def filterGenes(s, pattern): 129 def filterGenes(s, pattern):
126 if type(s) is not str: 130 if type(s) is not str:
127 return "NA" 131 return "NA"
128 res = pattern.search(s) 132 res = pattern.search(s)
129 if res: 133 if res: