Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 19:672d5e010b1f draft

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Uploaded
author davidvanzessen
date Fri, 25 Dec 2015 05:35:06 -0500
parents 431797cd74c8
children 0f6885b14628
files experimental_design.xml experimental_design/experimental_design.py imgt_loader/imgt_loader.py report_clonality/RScript.r
diffstat 4 files changed, 23 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/experimental_design.xml	Mon Dec 21 07:23:37 2015 -0500
+++ b/experimental_design.xml	Fri Dec 25 05:35:06 2015 -0500
@@ -19,7 +19,7 @@
 		</repeat>
 	</inputs>
 	<outputs>
-		<data format="tabular" name="out_file" />
+		<data format="tabular" name="out_file"/>
 	</outputs>
 	<help>
 Takes the ARGalaxy proprietary format and merges several samples and/or patients together.
--- a/experimental_design/experimental_design.py	Mon Dec 21 07:23:37 2015 -0500
+++ b/experimental_design/experimental_design.py	Fri Dec 25 05:35:06 2015 -0500
@@ -22,7 +22,13 @@
 				blast_files += 1
 			files.append(df)
 	patients[sample_id] = files
-	columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Functionality', 'V-REGION identity %', 'V-REGION identity nt', 'D-REGION reading frame', 'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', '5J-REGION trimmed-nt nb', u'Sample', u'Replicate']
+	columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', 
+			   u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Functionality', 'V-REGION identity %', 
+			   'V-REGION identity nt', 'D-REGION reading frame', 'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 
+			   'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 
+			   'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', '5J-REGION trimmed-nt nb', u'Sample', u'Replicate']
+	if "N-REGION-nt nb" in files[0].columns:
+		columns.insert(30, "N-REGION-nt nb")
 	if blast_files is not 0:
 		print "Has a parsed blastn file, using limited columns."
 		columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Sample', u'Replicate']
--- a/imgt_loader/imgt_loader.py	Mon Dec 21 07:23:37 2015 -0500
+++ b/imgt_loader/imgt_loader.py	Fri Dec 25 05:35:06 2015 -0500
@@ -26,7 +26,8 @@
 
 added_summary_columns = [u'Functionality', u'V-REGION identity %', u'V-REGION identity nt', u'D-REGION reading frame', u'AA JUNCTION', u'Functionality comment', u'Sequence']
 added_sequence_columns = [u'FR1-IMGT', u'FR2-IMGT', u'FR3-IMGT', u'CDR3-IMGT', u'JUNCTION', u'J-REGION', u'FR4-IMGT']
-added_junction_columns = [u"P3'V-nt nb", u'N1-REGION-nt nb', u"P5'D-nt nb", u"P3'D-nt nb", u'N2-REGION-nt nb', u"P5'J-nt nb", u"3'V-REGION trimmed-nt nb", u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb"]
+added_junction_columns = [u"P3'V-nt nb", u'N-REGION-nt nb', u'N1-REGION-nt nb', u"P5'D-nt nb", u"P3'D-nt nb", u'N2-REGION-nt nb', u"P5'J-nt nb", u"3'V-REGION trimmed-nt nb", 
+						  u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb"]
 
 outFile = args.output
 
@@ -63,7 +64,11 @@
 
 outFrame = tmp
 
-outFrame.columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Functionality', 'V-REGION identity %', 'V-REGION identity nt', 'D-REGION reading frame', 'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', '5J-REGION trimmed-nt nb']
+outFrame.columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', 
+					u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Functionality', 'V-REGION identity %', 'V-REGION identity nt', 'D-REGION reading frame', 
+					'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb', 
+					'N-REGION-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', 
+					'5J-REGION trimmed-nt nb']
 
 """
 IGHV[0-9]-[0-9ab]+-?[0-9]?D?
--- a/report_clonality/RScript.r	Mon Dec 21 07:23:37 2015 -0500
+++ b/report_clonality/RScript.r	Fri Dec 25 05:35:06 2015 -0500
@@ -584,6 +584,14 @@
 if(all(imgtcolumns %in% colnames(inputdata)))
 {
   print("found IMGT columns, running junction analysis")
+  
+  if(locus %in% c("IGK","IGL", "TRA", "TRG")){
+	  print("VJ recombination, using N column for junction analysis")
+	  print(names(PRODF))
+	  print(head(PRODF$N.REGION.nt.nb, 30))
+	  PRODF$N1.REGION.nt.nb = PRODF$N.REGION.nt.nb
+  }
+  
   newData = data.frame(data.table(PRODF)[,list(unique=.N, 
                                                VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
                                                P1=mean(.SD$P3V.nt.nb, na.rm=T),