Mercurial > repos > davidvanzessen > imgt_immunerepertoire_igg
changeset 1:9cf5050738ca draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 11 Mar 2014 09:16:12 -0400 |
| parents | 3cce6e04b1e8 |
| children | 84a386d96452 |
| files | RScript.r imgtconvert.py |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/RScript.r Thu Jan 23 08:35:31 2014 -0500 +++ b/RScript.r Tue Mar 11 09:16:12 2014 -0400 @@ -26,8 +26,7 @@ library(data.table) -t -read.table(inFile, sep="\t", header=TRUE, fill=T, comment.char="") +test = read.table(inFile, sep="\t", header=TRUE, fill=T, comment.char="") test = test[test$Sample != "",]
--- a/imgtconvert.py Thu Jan 23 08:35:31 2014 -0500 +++ b/imgtconvert.py Tue Mar 11 09:16:12 2014 -0400 @@ -1,4 +1,5 @@ import pandas as pd +pd.options.mode.chained_assignment = None # default='warn' import re import argparse import os @@ -135,4 +136,4 @@ 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")