Mercurial > repos > davidvanzessen > sff_extract_demultiplex
comparison r_wrapper.sh @ 0:25cd500a0852 draft
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| author | davidvanzessen |
|---|---|
| date | Thu, 08 May 2014 04:17:59 -0400 |
| parents | |
| children | afddfd016ba6 |
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| -1:000000000000 | 0:25cd500a0852 |
|---|---|
| 1 #!/bin/bash | |
| 2 input=$1 | |
| 3 output=$2 | |
| 4 outDir=$3 | |
| 5 mkdir $outDir | |
| 6 EOL=$4 | |
| 7 mismatches=$5 | |
| 8 partial=$6 | |
| 9 name=$(basename "$7") | |
| 10 ext="${name##*.}" | |
| 11 name="${name%.*}" | |
| 12 prefix=$name"_" | |
| 13 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 14 | |
| 15 for ((i=8;i<=$#;i=i+2)) | |
| 16 do | |
| 17 j=$((i+1)) | |
| 18 echo -e "${!i}\t${!j}" >> $outDir/barcodes.txt | |
| 19 done | |
| 20 | |
| 21 cd $outDir | |
| 22 echo "$3" | |
| 23 result=`$dir/sff2fastq $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial` | |
| 24 echo "$result" | tail -n +2 | sed 's/\t/,/g' > output.txt | |
| 25 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>" >> $output | |
| 26 ls | |
| 27 while IFS=, read barcode count location | |
| 28 do | |
| 29 if [ "total" == "$barcode" ] | |
| 30 then | |
| 31 echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td></tr>" >> $output | |
| 32 break | |
| 33 fi | |
| 34 file=$name"_"$barcode | |
| 35 cat $file.fastq | perl -e '$i=0;while(< >){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $file.fasta | |
| 36 cat $file.fastq | |
| 37 echo "<tr><td>$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 | |
| 38 done < output.txt | |
| 39 echo "</tbody></body></html>" >> $output |