Mercurial > repos > davidvanzessen > mutation_analysis

changeset 121:31cca6d3722a draft

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Uploaded
author davidvanzessen
date Wed, 17 Aug 2016 07:30:32 -0400
parents 613278c1bde0
children 3d64b3efd352
files mutation_analysis.xml wrapper.sh
diffstat 2 files changed, 15 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/mutation_analysis.xml	Tue Aug 16 09:10:50 2016 -0400
+++ b/mutation_analysis.xml	Wed Aug 17 07:30:32 2016 -0400
@@ -61,6 +61,11 @@
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		</data>
 	</outputs>
+	<citations>
+		<citation type="doi">10.1093/nar/gks457</citation>
+		<citation type="doi">10.1093/bioinformatics/btv359</citation>
+		<citation type="doi">10.1186/1471-2105-10-421</citation>
+	</citations>
 	<help>
 		Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.  
 		
--- a/wrapper.sh	Tue Aug 16 09:10:50 2016 -0400
+++ b/wrapper.sh	Wed Aug 17 07:30:32 2016 -0400
@@ -195,7 +195,6 @@
 
 mkdir $outdir/sequence_overview
 
-#Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
 
 echo "<table border='1'>" > $outdir/base_overview.html
@@ -206,12 +205,12 @@
 done < $outdir/sequence_overview/ntoverview.txt
 
 echo "<html><center><h1>$title</h1></center>" > $output
+echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
 echo "<script type='text/javascript' src='script.js'></script>" >> $output
 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
-
-#display the matched/unmatched for clearity
+echo "<link rel='stylesheet' href='http://yui.yahooapis.com/pure/0.6.0/pure-min.css'>" >> $output
 
 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
@@ -238,8 +237,8 @@
 	
 	cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
 
-	echo "<table border='1' width='100%'><caption><h3><a href='data_${func}.txt'>${func} table</a></h3></caption>" >> $output
-	echo "<tr><th>info</th>" >> $output
+	echo "<table class='pure-table pure-table-striped'>" >> $output
+	echo "<thead><tr><th>info</th>" >> $output
 	for gene in ${genes[@]}
 	do
 		tmp=`cat $outdir/${gene}_${func}_n.txt`
@@ -249,7 +248,7 @@
 	tmp=`cat $outdir/all_${func}_n.txt`
 	echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
 	tmp=`cat $outdir/unmatched_${func}_n.txt`
-	echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th>" >> $output
+	echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
 
 	while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
 	do
@@ -294,7 +293,7 @@
 	echo "<td><h1>${gene}</h1></td>" >> $output
 	echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
 	echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
-	echo "<td><table border='1'>" >> $output
+	echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output
 	while IFS=, read from a c g t
 		do
 			echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
@@ -308,7 +307,7 @@
 echo "<td><h1>All</h1></td>" >> $output
 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
-echo "<td><table border='1'>" >> $output
+echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output
 while IFS=, read from a c g t
 	do
 		echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
@@ -358,7 +357,8 @@
 
 echo "<div class='tabbertab' title='Downloads'>" >> $output
 
-echo "<table border='1' width='700px'>" >> $output
+echo "<table class='pure-table pure-table-striped'>" >> $output
+echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output
@@ -367,7 +367,7 @@
 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>Download</a></td></tr>" >> $output
 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output
-echo "<tr><td>Baseline PDF (<href a='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf'>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</a></td></tr>" >> $output
 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output