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view wrapper.sh @ 50:8ba6afa1247a draft

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author davidvanzessen
date Thu, 28 Jan 2016 09:21:25 -0500
parents 5c6b9e99d576
children d3542f87a304
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#!/bin/bash
set -e
dir="$(cd "$(dirname "$0")" && pwd)"
input=$1
method=$2
output=$3
outdir=$4
title=$5
include_fr1=$6
functionality=$7
unique=$8
naive_output=$9
mkdir $outdir

type="`file $input`"
if [[ "$type" == *"Zip archive"* ]] ; then
	echo "Zip archive"
	echo "unzip $input -d $PWD/files/"
	unzip $input -d $PWD/files/
elif [[ "$type" == *"XZ compressed data"* ]] ; then
	echo "ZX archive"
	echo "tar -xJf $input -C $PWD/files/"
	mkdir -p $PWD/files/$title
	tar -xJf $input -C $PWD/files/$title
fi

cat $PWD/files/*/1_* > $PWD/summary.txt
cat $PWD/files/*/3_* > $PWD/sequences.txt
cat $PWD/files/*/5_* > $PWD/aa.txt
cat $PWD/files/*/6_* > $PWD/junction.txt
cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
cat $PWD/files/*/8_* > $PWD/mutationstats.txt
cat $PWD/files/*/10_* > $PWD/hotspots.txt

#BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"

echo "${BLASTN_DIR}"

echo "identification ($method)"

if [[ "${method}" == "custom" ]] ; then
	python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
else
	ID_index=$(cat $PWD/summary.txt | grep -o -P ".+Sequence ID" | grep -o -P "\t" | wc -l)
	ID_index=$((ID_index+1))
	sequence_index=$(cat $PWD/summary.txt | grep -o -P ".+\tSequence" | grep -o -P "\t" | wc -l)
	sequence_index=$((sequence_index+1))
	
	echo "$ID_index ${sequence_index}"
	
	cat $PWD/summary.txt | tail -n+2 | cut -f ${ID_index},${sequence_index} | awk '{print ">" $1 "\n" $2}' > $PWD/sequences.fasta
	
	echo -e "qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore" > $outdir/identified_genes.txt
	${BLASTN_DIR}/blastn -task blastn -db $dir/subclass_definition.db -query $PWD/sequences.fasta -outfmt 6 >> $outdir/identified_genes.txt
fi



echo "merging"
Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique

genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
echo "R mutation analysis"
Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
echo "python mutation analysis"
python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
echo "R AA histogram"
Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt

genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)


echo "<html><center><h1>$title</h1></center><table border='1'>" > $output
echo "<tr><th>info</th>" >> $output
for gene in ${genes[@]}
do
	tmp=`cat $outdir/${gene}_n.txt`
	echo "<th><a href='matched_${gene}.txt'>${gene} (N = $tmp)</a></th>" >> $output
done
tmp=`cat $outdir/total_n.txt`
echo "<th><a href='matched_all.txt'>all (N = $tmp)</a></th>" >> $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 allx ally allz
do
	if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh
		echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output
	else
		echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
	fi
done < $outdir/result.txt
echo "</table>" >> $output
echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br /><a href='merged.txt'>all data</a><br /><a href='mutation_by_id.txt'>mutations by id</a><br /><a href='aa_id_mutations.txt'>AA mutations location by id</a><br /><a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output


echo "<img src='all.png'/><br />" >> $output
echo "<a href='all.txt'>download data</a><br />" >> $output
if [ -a $outdir/ca.png ] 
then
	echo "<img src='ca.png'/><br />" >> $output
	echo "<a href='ca.txt'>download data</a><br />" >> $output
fi
if [ -a $outdir/cg.png ]
then
	echo "<img src='cg.png'/><br />" >> $output
	echo "<a href='cg.txt'>download data</a><br />" >> $output
fi
if [ -a $outdir/scatter.png ]
then
	echo "<img src='scatter.png'/><br />" >> $output
	echo "<a href='scatter.txt'>download data</a><br />" >> $output
fi
if [ -a $outdir/frequency_ranges.png ]
then
	echo "<img src='frequency_ranges.png'/><br />" >> $output
	echo "<a href='frequency_ranges_classes.txt'>download class data</a><br />" >> $output
	echo "<a href='frequency_ranges_subclasses.txt'>download subclass data</a><br />" >> $output
fi
if [ -a $outdir/aa_histogram.png ]
then
	echo "<img src='aa_histogram.png'/><br />" >> $output
	echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output
fi

for gene in ${genes[@]}
do
	echo "<table border='1'><caption>$gene transition table</caption>" >> $output
	while IFS=, read from a c g t
		do
			echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
	done < $outdir/transitions_${gene}.txt
	echo "</table>" >> $output
done

echo "<table border='1'><caption>All transition table</caption>" >> $output
while IFS=, read from a c g t
	do
		echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
done < $outdir/transitions.txt
echo "</table>" >> $output

echo "</html>" >> $output


#optional output for naive

if [[ "$naive_output" != "None" ]]
then
	echo "naive_output: $naive_output"
	#python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output} 2>&1
	Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1
fi











#rm $outdir/HS12RSS.txt
#rm $outdir/HS23RSS.txt