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Curtis dev
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| #!/bin/bash | ||
| #$ -o prepSample.log | ||
| #$ -e prepSample.err | ||
| #$ -j y | ||
| #$ -N wtdbg2 | ||
| #$ -pe smp 2-16 | ||
| #$ -V -cwd | ||
| set -e | ||
|
|
||
| #This function will check to make sure the directory doesn't already exist before trying to create it | ||
| make_directory() { | ||
| if [ -e $1 ]; then | ||
| echo "Directory "$1" already exists" | ||
| else | ||
| mkdir $1 | ||
| echo "Directory "$1" has been created" | ||
| fi | ||
| } | ||
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||
| source /etc/profile.d/modules.sh | ||
| module purge | ||
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| NSLOTS=${NSLOTS:=24} | ||
| echo '$NSLOTS is set to:' $NSLOTS | ||
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| FASTQDIR=$1 | ||
| echo '$FASTQDIR is set to:' $FASTQDIR | ||
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| set -u | ||
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| if [ "$FASTQDIR" == "" ]; then | ||
| echo "" | ||
| echo "Usage: $0 barcode-fastq-dir" | ||
| echo "" | ||
| exit 1; | ||
| fi; | ||
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| # Setup any debugging information | ||
| date | ||
| hostname | ||
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| # Setup tempdir | ||
| tmpdir=$(mktemp -p . -d prepfastq.XXXXXX) | ||
| trap ' { echo "END - $(date)"; rm -rf $tmpdir; } ' EXIT | ||
| make_directory $tmpdir/log | ||
| echo "$0: temp dir is $tmpdir"; | ||
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| dir=$FASTQDIR | ||
| echo '$dir is set to:' $dir | ||
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| BARCODE=$(basename ${dir}) | ||
| echo '$BARCODE is set to:' $BARCODE | ||
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| # check to see if reads have been compresesd and renamed to all-barcodeXX.fastq.gz | ||
| if [[ -e ${dir}/all-${BARCODE}.fastq.gz ]]; then | ||
| echo "Reads have been concatenated and renamed by 03_prepSample script already. Exiting...." | ||
| exit 0 | ||
| fi | ||
|
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| ### commented out since gzipping is done by previous script | ||
| # Gzip them all | ||
| #uncompressed=$(\ls $dir/*.fastq 2>/dev/null || true) | ||
| #if [ "$uncompressed" != "" ]; then | ||
| # echo "$uncompressed" | xargs -P $NSLOTS gzip | ||
| #fi | ||
|
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||
| # Put all the individual gzip fastqs into a subdir, | ||
| # Concatenate them, and then remove them. | ||
| # Keep the aggregate fastq file. | ||
| echo "concatenating .fastq.gz files in barcode sub-dir..." | ||
| mkdir -p ${dir}/fastqChunks | ||
| mv ${dir}/*.fastq.gz ${dir}/fastqChunks | ||
| cat ${dir}/fastqChunks/*.fastq.gz > ${dir}/all-${BARCODE}.fastq.gz | ||
| rm -rf $dir/fastqChunks | ||
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| # Combine reads and count lengths in one stream | ||
| echo "combining reads and counting read lengths..." | ||
| LENGTHS=${dir}/readlengths.txt.gz | ||
| zcat ${dir}/all-${BARCODE}.fastq.gz | perl -lne ' | ||
| next if($. % 4 != 2); | ||
| print length($_); | ||
| ' | sort -rn | gzip -cf > ${LENGTHS}; | ||
| echo "Finished combining reads and counting read lengths." | ||
|
|
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