Mercurial > repos > davidvanzessen > sff_extract_demultiplex
comparison wrapper.sh @ 5:35b55f1c0c59 draft
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| author | davidvanzessen |
|---|---|
| date | Tue, 08 Jul 2014 09:38:54 -0400 |
| parents | |
| children | 18ede27dc6b0 |
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| 4:8e3d95d7f342 | 5:35b55f1c0c59 |
|---|---|
| 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 unzip $dir/fastqc_v0.11.2.zip -d $PWD/ > $PWD/unziplog.log | |
| 16 chmod 755 $PWD/FastQC/fastqc | |
| 17 | |
| 18 declare -A trim_start | |
| 19 declare -A trim_end | |
| 20 for ((i=8;i<=$#;i=i+4)) | |
| 21 do | |
| 22 j=$((i+1)) | |
| 23 start_int=$((i+2)) | |
| 24 end_int=$((i+3)) | |
| 25 id="${!i}" | |
| 26 echo "$id" | |
| 27 trim_start[$id]=${!start_int} | |
| 28 trim_end[$id]=${!end_int} | |
| 29 echo -e "$id\t${!j}" >> $outDir/barcodes.txt | |
| 30 | |
| 31 done | |
| 32 trim_start["unmatched"]=0 | |
| 33 trim_end["unmatched"]=0 | |
| 34 | |
| 35 echo "trim_start = ${trim_start[@]}" | |
| 36 echo "trim_end = ${trim_end[@]}" | |
| 37 | |
| 38 workdir=$PWD | |
| 39 cd $outDir | |
| 40 echo "$3" | |
| 41 result=`$dir/sff2fastq $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial` | |
| 42 echo "$result" | tail -n +2 | sed 's/\t/,/g' > output.txt | |
| 43 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><th>Trimmed FASTA</th><th>FASTQC</th></tr></thead><tbody>" >> $output | |
| 44 while IFS=, read barcode count location | |
| 45 do | |
| 46 if [ "total" == "$barcode" ] | |
| 47 then | |
| 48 echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td><td></td><td></td><td></td><td></td></tr>" >> $output | |
| 49 break | |
| 50 fi | |
| 51 file=$name"_"$barcode | |
| 52 mkdir $outDir/fastqc_$barcode | |
| 53 $workdir/FastQC/fastqc $file.fastq -o $outDir 2> /dev/null | |
| 54 cat $file.fastq | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > $file.fasta | |
| 55 python $dir/trim.py --input $file.fasta --output ${file}_trimmed.fasta --start ${trim_start[$barcode]} --end ${trim_end[$barcode]} | |
| 56 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><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td><td><a href='${name}_${barcode}_fastqc.html'>Report</a></td></tr>" >> $output | |
| 57 done < output.txt | |
| 58 echo "</tbody></body></html>" >> $output |