changeset 18:949a30f04d9b draft

Uploaded

--- a/merge_and_filter.r	Thu Nov 24 10:24:19 2016 -0500
+++ b/merge_and_filter.r	Mon Nov 28 04:41:22 2016 -0500
@@ -96,8 +96,6 @@
 result$JGene = gsub("^Homsap ", "", result$J.GENE.and.allele)
 result$JGene = gsub("[*].*", "", result$JGene)
 
-print(result[result$Sequence.ID == "JY8QFUQ01C310D",c("Sequence.ID","best_match")])
-
 splt = strsplit(class.filter, "_")[[1]]
 chunk_hit_threshold = as.numeric(splt[1])
 nt_hit_threshold = as.numeric(splt[2])
@@ -112,8 +110,6 @@
 	result$best_match = "all"
 }
 
-print(result[result$Sequence.ID == "JY8QFUQ01C310D",c("Sequence.ID","best_match")])
-
 write.table(x=result, file=gsub("merged.txt$", "before_filters.txt", output), sep="\t",quote=F,row.names=F,col.names=T)
 
 print(paste("Number of empty CDR1 sequences:", sum(result$CDR1.IMGT.seq == "")))
@@ -139,8 +135,6 @@
 	filtering.steps = rbind(filtering.steps, c("After empty CDR2, FR3 filter", nrow(result)))
 }
 
-print(result[result$Sequence.ID == "JY8QFUQ01C310D",c("Sequence.ID","best_match")])
-
 if(empty.region.filter == "leader"){
 	result = result[!(grepl("n|N", result$FR1.IMGT.seq) | grepl("n|N", result$FR2.IMGT.seq) | grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR1.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),]
 } else if(empty.region.filter == "FR1"){
@@ -151,9 +145,6 @@
 	result = result[!(grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),]
 }
 
-print(result[result$Sequence.ID == "JY8QFUQ01C310D",c("Sequence.ID","best_match")])
-print(result[result$Sequence.ID == "JY8QFUQ01BNS72",c("Sequence.ID","best_match")])
-
 print(paste("Number of sequences in result after n filtering:", nrow(result)))
 filtering.steps = rbind(filtering.steps, c("After N filter", nrow(result)))
 
@@ -192,9 +183,6 @@
 	result = result[!duplicated(result$unique.def),]
 }
 
-print(result[result$Sequence.ID == "JY8QFUQ01C310D",c("Sequence.ID","best_match")])
-print(result[result$Sequence.ID == "JY8QFUQ01BNS72",c("Sequence.ID","best_match")])
-
 write.table(result, gsub("before_unique_filter.txt", "after_unique_filter.txt", before.unique.file), sep="\t", quote=F,row.names=F,col.names=T)
 
 filtering.steps = rbind(filtering.steps, c("After filter unique sequences", nrow(result)))
@@ -217,11 +205,6 @@
 
 result = result[!(duplicated(result$past)), ]
 
-
-
-print(result[result$Sequence.ID == "JY8QFUQ01C310D",c("Sequence.ID","best_match")])
-
-
 result = result[,!(names(result) %in% c("past", "best_match_class"))]
 
 print(paste("Number of sequences in result after", unique.type, "filtering:", nrow(result)))

--- a/shm_csr.xml	Thu Nov 24 10:24:19 2016 -0500
+++ b/shm_csr.xml	Mon Nov 28 04:41:22 2016 -0500
@@ -33,13 +33,15 @@
 			<option value="CDR3.IMGT.seq">CDR3 (nt)</option>
 			<option value="Sequence.ID" selected="true">Don't remove duplicates</option>
 		</param>
-		<param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
-			<option value="70_70" selected="true">>70% class and >70% subclass</option>
-			<option value="60_55">>60% class and >55% subclass</option>
-			<option value="70_0">>70% class</option>
-			<option value="60_0">>60% class</option>
-			<option value="101_101">Do not assign (sub)class</option>
-		</param>
+		<conditional name="class_filter_cond">
+			<param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
+				<option value="70_70" selected="true">>70% class and >70% subclass</option>
+				<option value="60_55">>60% class and >55% subclass</option>
+				<option value="70_0">>70% class</option>
+				<option value="60_0">>60% class</option>
+				<option value="101_101">Do not assign (sub)class</option>
+			</param>
+		</conditional>
 		<conditional name="naive_output_cond">
 			<param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
 				<option value="yes">Yes</option>
@@ -59,15 +61,23 @@
 		<data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
 		<data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
+		</data>
+		<data format="imgt_archive" name="naive_output_ca" label = "Naive input data from ${in_file.name}" >
+		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>class_filter_cond['class_filter'] == "101_101"</filter>
 		</data>
 	</outputs>
 	<citations>

--- a/wrapper.sh	Thu Nov 24 10:24:19 2016 -0500
+++ b/wrapper.sh	Mon Nov 28 04:41:22 2016 -0500
@@ -651,10 +651,15 @@
 
 if [[ "$naive_output" == "yes" ]]
 then
-	cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
-	cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
-	cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
-	cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
+	if [[ "${class_filter}" == "101_101" ]]
+	then
+		cp $outdir/new_IMGT.txz ${naive_output_ca}
+	else
+		cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
+		cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
+		cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
+		cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
+	fi
 fi
 
 echo "</table>" >> $outdir/base_overview.html