Mercurial > repos > davidvanzessen > sff_extract_demultiplex
diff r_wrapper.sh @ 0:25cd500a0852 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 08 May 2014 04:17:59 -0400 |
| parents | |
| children | afddfd016ba6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_wrapper.sh Thu May 08 04:17:59 2014 -0400 @@ -0,0 +1,39 @@ +#!/bin/bash +input=$1 +output=$2 +outDir=$3 +mkdir $outDir +EOL=$4 +mismatches=$5 +partial=$6 +name=$(basename "$7") +ext="${name##*.}" +name="${name%.*}" +prefix=$name"_" +dir="$(cd "$(dirname "$0")" && pwd)" + +for ((i=8;i<=$#;i=i+2)) +do + j=$((i+1)) + echo -e "${!i}\t${!j}" >> $outDir/barcodes.txt +done + +cd $outDir +echo "$3" +result=`$dir/sff2fastq $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial` +echo "$result" | tail -n +2 | sed 's/\t/,/g' > output.txt +echo "<html><head><title>$name demultiplex</title></head><body><table border='1'><thead><tr><th>ID</th><th>Count</th><th>FASTQ</th><th>FASTA</th></tr></thead><tbody>" >> $output +ls +while IFS=, read barcode count location + do + if [ "total" == "$barcode" ] + then + echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td></tr>" >> $output + break + fi + file=$name"_"$barcode + cat $file.fastq | perl -e '$i=0;while(< >){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $file.fasta + cat $file.fastq + echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td></tr>" >> $output +done < output.txt +echo "</tbody></body></html>" >> $output