# HG changeset patch
# User davidvanzessen
# Date 1404740939 14400
# Node ID 387fce4a1dd41a0b87f0283e8fb2cb53c1f17883
# Parent  021d39f6bb0ee6698460bfdd808f86aeb8813a91
Uploaded

diff -r 021d39f6bb0e -r 387fce4a1dd4 imgtconvert.py
--- a/imgtconvert.py	Fri Jun 06 04:34:44 2014 -0400
+++ b/imgtconvert.py	Mon Jul 07 09:48:59 2014 -0400
@@ -47,9 +47,9 @@
 
 outFile = args.output
 
-fSummary = pd.read_csv(triplets[0][0], sep="\t")
-fSequence = pd.read_csv(triplets[0][1], sep="\t")
-fJunction = pd.read_csv(triplets[0][2], sep="\t")
+fSummary = pd.read_csv(triplets[0][0], sep="\t", low_memory=False)
+fSequence = pd.read_csv(triplets[0][1], sep="\t", low_memory=False)
+fJunction = pd.read_csv(triplets[0][2], sep="\t", low_memory=False)
 tmp = fSummary[["Sequence ID", "JUNCTION frame", "V-GENE and allele", "D-GENE and allele", "J-GENE and allele"]]
 
 tmp["CDR1 Seq"] = fSequence["CDR1-IMGT"]
@@ -186,5 +186,6 @@
 outFrame["VDJ Frame"] = tmp
 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 = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows?
+#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")
diff -r 021d39f6bb0e -r 387fce4a1dd4 imgtconvert.sh
--- a/imgtconvert.sh	Fri Jun 06 04:34:44 2014 -0400
+++ b/imgtconvert.sh	Mon Jul 07 09:48:59 2014 -0400
@@ -43,7 +43,7 @@
 then
 	echo "Zip archive"
 	echo "Trying: unzip $1 -d $PWD/files/"
-	unzip $1 -d $PWD/files/
+	unzip $1 -d $PWD/files/ > $PWD/unziplog.log
 fi
 
 if [[ "$f" == *"$rarType"* ]]