Mercurial > repos > davidvanzessen > sff_extract_demultiplex

comparison wrapper.sh @ 13:7843e05bbb6c draft default tip

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author davidvanzessen
date Wed, 25 Nov 2015 09:44:30 -0500
parents 4b85fd44d946
children
comparison
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12:4b85fd44d946 13:7843e05bbb6c
8 partial="$6" 8 partial="$6"
9 name=$(basename "$7") 9 name=$(basename "$7")
10 ext="${name##*.}" 10 ext="${name##*.}"
11 name="${name%.*}" 11 name="${name%.*}"
12 name="${name// /_}" 12 name="${name// /_}"
13 prefix="$name\"_\"" 13 prefix="${name}_"
14 dir="$(cd "$(dirname "$0")" && pwd)" 14 dir="$(cd "$(dirname "$0")" && pwd)"
15 15
16 unzip $dir/fastqc_v0.11.2.zip -d $PWD/ > $PWD/unziplog.log 16 unzip $dir/fastqc_v0.11.2.zip -d $PWD/ > $PWD/unziplog.log
17 chmod 755 $PWD/FastQC/fastqc 17 chmod 755 $PWD/FastQC/fastqc
18 18
55 if [ "total" == "$barcode" ] 55 if [ "total" == "$barcode" ]
56 then 56 then
57 echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td><td></td><td></td><td></td><td></td></tr>" >> $output 57 echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td><td></td><td></td><td></td><td></td></tr>" >> $output
58 break 58 break
59 fi 59 fi
60 file=$name"_"$barcode 60 file="${name}_${barcode}"
61 mkdir $outDir/fastqc_$barcode 61 mkdir "$outDir/fastqc_$barcode"
62 $workdir/FastQC/fastqc $file.fastq -o $outDir 2> /dev/null 62 $workdir/FastQC/fastqc "$file.fastq" -o "$outDir" 2> /dev/null
63 cat "$file.fastq" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$file.fasta" 63 cat "$file.fastq" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$file.fasta"
64 python $dir/trim.py --input "$file.fasta" --output "${file}_trimmed.fasta" --start "${trim_start[$barcode]}" --end "${trim_end[$barcode]}" 64 python $dir/trim.py --input "$file.fasta" --output "${file}_trimmed.fasta" --start "${trim_start[$barcode]}" --end "${trim_end[$barcode]}"
65 echo "<tr><td>$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>" >> $output 65 echo "<tr><td>$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
66 done < output.txt 66 done < output.txt
67 echo "</tbody></body></html>" >> $output 67 echo "</tbody></body></html>" >> $output