Mercurial > repos > davidvanzessen > shm_csr

changeset 29:80c4eebf7bc9 draft

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Uploaded
author davidvanzessen
date Thu, 08 Dec 2016 04:51:09 -0500
parents c0ecc31829bd
children 33a7c49d48a7
files aa_histogram.r shm_csr.xml wrapper.sh
diffstat 3 files changed, 15 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/aa_histogram.r	Wed Dec 07 08:17:09 2016 -0500
+++ b/aa_histogram.r	Thu Dec 08 04:51:09 2016 -0500
@@ -16,15 +16,15 @@
 
 for(gene in genes){
 	if(gene == ""){
-			mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
-			absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
+		mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
+		absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
 	} else {
-			mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
-			absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
+		mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
+		absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
 	}
 	print(paste("nrow", gene, nrow(absent.aa.by.id.gene)))
 	if(nrow(mutations.by.id.gene) == 0){
-			next
+		next
 	}
 
 	mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)])
--- a/shm_csr.xml	Wed Dec 07 08:17:09 2016 -0500
+++ b/shm_csr.xml	Thu Dec 08 04:51:09 2016 -0500
@@ -27,7 +27,7 @@
 			<option value="CDR3.IMGT.AA,best_match_class">CDR3 (AA), C region</option>
 			<option value="CDR3.IMGT.AA">CDR3 (AA)</option>
 			
-			<option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3.nt.Seq, C region</option>
+			<option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3 (nt), C region</option>
 			<option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
 			<option value="CDR3.IMGT.seq,best_match_class">CDR3 (nt), C region</option>
 			<option value="CDR3.IMGT.seq">CDR3 (nt)</option>
--- a/wrapper.sh	Wed Dec 07 08:17:09 2016 -0500
+++ b/wrapper.sh	Thu Dec 08 04:51:09 2016 -0500
@@ -187,6 +187,9 @@
 if [ -e "$outdir/aa_histogram_.png" ]; then
         mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
         mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
+        mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
+        mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
+        mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
 fi
 
 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
@@ -592,6 +595,12 @@
 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
 
+echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output
+echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output
+
 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output