Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

changeset 4:f11df36f43bb draft

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Uploaded
author davidvanzessen
date Mon, 15 Sep 2014 05:37:16 -0400
parents f9316f7676cc
children 9641f3dfc590
files RScript.r wrapper.sh
diffstat 2 files changed, 74 insertions(+), 36 deletions(-) [+]
line wrap: on
line diff
--- a/RScript.r	Tue Aug 26 09:53:22 2014 -0400
+++ b/RScript.r	Mon Sep 15 05:37:16 2014 -0400
@@ -8,10 +8,11 @@
 
 cat("<html><table><tr><td>Starting analysis</td></tr>", file=logfile, append=F)
 
-require(ggplot2)
-require(reshape2)
-require(data.table)
-require(grid)
+library(ggplot2)
+library(reshape2)
+library(data.table)
+library(grid)
+library(parallel)
 #require(xtable)
 cat("<tr><td>Reading input</td></tr>", file=logfile, append=T)
 dat = read.csv(inFile, sep="\t")
@@ -33,7 +34,9 @@
 cat("<tr><td>Removing duplicates</td></tr>", file=logfile, append=T)
 dat = dat[!duplicated(dat$paste),]
 patients = split(dat, dat$Patient, drop=T)
-intervalReads = rev(c(0,2,10,100,1000,10000))
+rm(dat)
+patients = patients[1:5]
+intervalReads = rev(c(0,10,25,50,100,1000,10000))
 intervalFreq = rev(c(0,0.01,0.1,0.5,1,5))
 V_Segments = c(".*", "IGHV", "IGHD", "IGKV", "IGKV", "IgKINTR", "TRGV", "TRDV", "TRDD" , "TRBV")
 J_Segments = c(".*", ".*", ".*", "IGKJ", "KDE", ".*", ".*", ".*", ".*", ".*")
@@ -48,9 +51,11 @@
     onShort = "freq"
   }
   splt = split(x, x$Sample, drop=T)
+  type="pair"
   if(length(splt) == 1){
     print(paste(paste(x[1,which(colnames(x) == "Patient")]), "has one sample"))
-    splt[[2]] = data.frame("Patient" = 'NA', "Receptor" = 'NA', "Sample" = 'NA', "Cell_Count" = 100, "Clone_Molecule_Count_From_Spikes" = 10, "Log10_Frequency" = 1, "Total_Read_Count" = 100, "dsMol_per_1e6_cells" = 100, "J_Segment_Major_Gene" = 'NA', "V_Segment_Major_Gene" = 'NA', "Clone_Sequence" = 'NA', "CDR3_Sense_Sequence" = 'NA', "Related_to_leukemia_clone" = FALSE, "Frequency"= 0, "normalized_read_count" = 0, "paste" = 'a')
+    splt[[2]] = data.frame("Patient" = character(0), "Receptor" = character(0), "Sample" = character(0), "Cell_Count" = numeric(0), "Clone_Molecule_Count_From_Spikes" = numeric(0), "Log10_Frequency" = numeric(0), "Total_Read_Count" = numeric(0), "dsMol_per_1e6_cells" = numeric(0), "J_Segment_Major_Gene" = character(0), "V_Segment_Major_Gene" = character(0), "Clone_Sequence" = character(0), "CDR3_Sense_Sequence" = character(0), "Related_to_leukemia_clone" = logical(0), "Frequency"= numeric(0), "normalized_read_count" = numeric(0), "paste" = character(0))
+    type="single"
   }
   patient1 = splt[[1]]
   patient2 = splt[[2]]
@@ -76,7 +81,7 @@
     switched = T
   }
   if(appendtxt){
-    cat(paste(patient, oneSample, twoSample, sep="\t"), file="patients.txt", append=T, sep="", fill=3)
+    cat(paste(patient, oneSample, twoSample, type, sep="\t"), file="patients.txt", append=T, sep="", fill=3)
   }
   cat(paste("<tr><td>", patient, "</td></tr>", sep=""), file=logfile, append=T)
   patientMerge = merge(patient1, patient2, by="Clone_Sequence")
@@ -107,21 +112,21 @@
     #threshhold = 0
     if(threshhold != 0){
       if(sum(one) > 0){
-        dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence")]
-        colnames(dfOne) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence")
+        dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
+        colnames(dfOne) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone")
         filenameOne = paste(oneSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
         write.table(dfOne, file=paste(filenameOne, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
       }
       if(sum(two) > 0){
-        dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence")]
-        colnames(dfTwo) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence")
+        dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
+        colnames(dfTwo) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone")
         filenameTwo = paste(twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
         write.table(dfTwo, file=paste(filenameTwo, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
       }
     }
     if(sum(both) > 0){
-      dfBoth = patientMerge[both,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "normalized_read_count.x", "Frequency.x", "Clone_Sequence", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "normalized_read_count.y", "Frequency.y")]
-      colnames(dfBoth) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Normalized_Read_Count", oneSample), paste("Frequency", oneSample), "Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Normalized_Read_Count", twoSample), paste("Frequency", twoSample))
+      dfBoth = patientMerge[both,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "normalized_read_count.x", "Frequency.x", "Related_to_leukemia_clone.x", "Clone_Sequence", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "normalized_read_count.y", "Frequency.y", "Related_to_leukemia_clone.y")]
+      colnames(dfBoth) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Normalized_Read_Count", oneSample), paste("Frequency", oneSample), paste("Related_to_leukemia_clone", oneSample),"Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Normalized_Read_Count", twoSample), paste("Frequency", twoSample), paste("Related_to_leukemia_clone", twoSample))
       filenameBoth = paste(oneSample, "_", twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
       write.table(dfBoth, file=paste(filenameBoth, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
     }
@@ -179,24 +184,24 @@
 
 interval = intervalFreq
 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
-product = data.frame("Titles"=rep(Titles, each=6), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=6), "J_Segments"=rep(J_Segments, each=6))
+product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
 #patientFrequencyCount(patient1)
 #lapply(patients[c(5,6,10)], FUN=patientFrequencyCount)
 #lapply(patients[c(5,6,7,8,13)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
 #lapply(patients[c(6,7,8)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
 #lapply(patients[c(6)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
-lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
+mclapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
 
 cat("<tr><td>Starting Cell Count analysis</td></tr>", file=logfile, append=T)
 
 interval = intervalReads
 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
-product = data.frame("Titles"=rep(Titles, each=6), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=6), "J_Segments"=rep(J_Segments, each=6))
+product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
 #patientResult = patientReadCount(patient1)
 #lapply(patients[c(5,6,10)], FUN=patientReadCount)
 #lapply(patients[c(5,6,7,8,13)], FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
 #lapply(patients[c(6)], FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
-lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
+mclapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
 
 cat("</table></html>", file=logfile, append=T)
 
--- a/wrapper.sh	Tue Aug 26 09:53:22 2014 -0400
+++ b/wrapper.sh	Mon Sep 15 05:37:16 2014 -0400
@@ -21,36 +21,42 @@
 
 cd $outputDir
 
-html="index.html"
-echo "<html><head><title>Result</title>" > $html
-echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $html
-echo "<script type='text/javascript' src='tabber.js'></script>" >> $html
-echo "<script type='text/javascript' src='script.js'></script>" >> $html
-echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $html
-echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $html
-echo "<div id='hidden_div' style='display: none;'></div>" >> $html
-echo "<div class='tabber'>" >> $html
-while read patient sample1 sample2
+header="<html><head><script type='text/javascript' src='jquery-1.11.0.min.js'></script><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'></head><div id='hidden_div' style='display: none;'></div>"
+singles=()
+pairs_BM_PB=()
+pairs_Left_Right=()
+pairs_R_Dx=()
+while read patient sample1 sample2 type
 do
 	echo "$patient"
+	html="${patient}.html"
+	echo "$header" > $html
+	if [[ "$type" == *pair* ]] ; then
+		if [[ "$sample1" == *_BM* ]] || [[ "$sample1" == *_PB* ]] ; then
+			pairs_BM_PB+=( "$patient" )
+		elif [[ "$sample1" == *_Left* ]] || [[ "$sample1" == *_Right* ]] ; then
+			pairs_Left_Right+=( "$patient" )
+		else
+			pairs_R_Dx+=( "$patient" )
+		fi
+	else
+		singles+=( "$patient" )
+	fi
 	oldLocus=""
 	sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
 	sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
 	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
-	echo "<div class='tabbertab' title='$patient'>" >> $html
 	echo "<div class='tabber'>" >> $html
 	echo "<div class='tabbertab' title='Data frequency'>" >> $html
 	echo "<table><tr><td style='vertical-align:top;'>" >> $html
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html
-	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Normalized Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Normalized Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
+	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
 	echo "<tbody>" >> $html
-	readsumtable="<table class='result_table summary_table'><thead><tr><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Total normalized read count for $sample1</th><th>Total normalized read count for $sample2</th></tr></thead>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
 			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
 			echo "<tr><td><b>$locus</b></td>" >> $html
-			readsumtable="${readsumtable}<tr><td>$locus</td><td>$v_segment</td><td>$j_segment</td><td>$locusreadsum1</td><td>$locusreadsum2</td></tr>"
 		else
 			echo "<td></td>" >> $html
 		fi
@@ -81,7 +87,7 @@
 	done < tmp.txt
 	echo "</tbody></table>" >> $html
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
-	echo "${readsumtable}</table></div>" >> $html
+	echo "</div>" >> $html
 	echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
 	echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html
 	echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> $html
@@ -93,13 +99,11 @@
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html
 	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
 	echo "<tbody>" >> $html
-	readsumtable="<table class='result_table summary_table'><thead><tr><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Total normalized read count for $sample1</th><th>Total normalized read count for $sample2</th></tr></thead>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
 			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
 			echo "<tr><td><b>$locus</b></td>" >> $html
-			readsumtable="${readsumtable}<tr><td>$locus</td><td>$v_segment</td><td>$j_segment</td><td>$locusreadsum1</td><td>$locusreadsum2</td></tr>"
 		else
 			echo "<td></td>" >> $html
 		fi
@@ -130,13 +134,42 @@
 	done < tmp.txt
 	echo "</tbody></table>" >> $html
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
-	echo "${readsumtable}</table></div>" >> $html
+	echo "</div>" >> $html
 	echo "<div class='tabbertab' title='Graphs reads'>" >> $html
 	echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
 	echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> $html
 	echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html
 	echo "</div>" >> $html
 	echo "</div>" >> $html
+	echo "</html>" >> $html
 done < patients.txt
-echo "</div></html>" >> $html
 rm tmp.txt
+
+html="index.html"
+echo "<html>" > $html
+echo "<table>" >> $html
+echo "<tr><td><b>Singles:</b></td></tr>" >> $html
+for patient in "${singles[@]}"
+do
+	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
+done
+echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> $html
+for patient in "${pairs_Left_Right[@]}"
+do
+	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
+done
+echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> $html
+for patient in "${pairs_BM_PB[@]}"
+do
+	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
+done
+echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> $html
+for patient in "${pairs_R_Dx[@]}"
+do
+	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
+done
+echo "<tr><td><b>Triplets:</b></td></tr>" >> $html
+
+echo "</table>" >> $html
+echo "</html>" >> $html
+