Mercurial > repos > davidvanzessen > imgt_loader_igg
changeset 3:191d0df65d28 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 11 Mar 2014 09:24:29 -0400 |
| parents | 477cab9c32d1 |
| children | 021d39f6bb0e |
| files | imgtconvert.py |
| diffstat | 1 files changed, 6 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- 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")