Distributed by Region (sh)
Distributed bash-interpreter apps use bash functions to declare entry points. Entry points are executed as subjobs on new workers with their own respective system requirements. This app has the following entry points specified as bash functions:
- main
- count_func
- sum_reads
The main function takes the initial
*.bam, generates an index *.bai if needed, and obtains the list of regions from the *.bam file. Every 10 regions will be sent, as input, to the count_func entry point using dx-jobutil-new-job command. regions=$(samtools view -H "${mappings_sorted_bam_name}" | grep "\@SQ" | sed 's/.*SN:\(\S*\)\s.*/\1/')
echo "Segmenting into regions"
count_jobs=()
counter=0
temparray=()
for r in $(echo $regions); do
if [[ "${counter}" -ge 10 ]]; then
echo "${temparray[@]}"
count_jobs+=($(dx-jobutil-new-job -ibam_file="${mappings_sorted_bam}" -ibambai_file="${mappings_sorted_bai}" "${temparray[@]}" count_func))
temparray=()
counter=0
fi
temparray+=("-iregions=${r}") # Here we add to an array of -i<parameter>'s
counter=$((counter+1))
done
if [[ counter -gt 0 ]]; then # Previous loop will miss last iteration if its < 10
echo "${temparray[@]}"
count_jobs+=($(dx-jobutil-new-job -ibam_file="${mappings_sorted_bam}" -ibambai_file="${mappings_sorted_bai}" "${temparray[@]}" count_func))
fi
Job outputs from the count_func entry point are referenced as Job Based Object References (JBOR) and used as inputs for the sum_reads entry point.
echo "Merge count files, jobs:"
echo "${count_jobs[@]}"
readfiles=()
for count_job in "${count_jobs[@]}"; do
readfiles+=("-ireadfiles=${count_job}:counts_txt")
done
echo "file name: ${sorted_bamfile_name}"
echo "Set file, readfile variables:"
echo "${readfiles[@]}"
countsfile_job=$(dx-jobutil-new-job -ifilename="${mappings_sorted_bam_prefix}" "${readfiles[@]}" sum_reads)
Job outputs of the sum_reads entry point is used as the output of the main entry point via JBOR reference in the
dx-jobutil-add-output command. echo "Specifying output file"
dx-jobutil-add-output counts_txt "${countsfile_job}:read_sum" --class=jobref
}
This entry point performs a SAMtools count of the 10 regions passed as input. This execution will be run on a new worker. As a result variables from other functions (e.g.
main()) will not be accessible here.Once the output file with counts is created, it is uploaded to the platform and assigned as the entry point’s job output
counts_txt via the command dx-jobutil-add-output.count_func() {
set -e -x -o pipefail
echo "Value of bam_file: '${bam_file}'"
echo "Value of bambai_file: '${bambai_file}'"
echo "Regions being counted '${regions[@]}'"
dx-download-all-inputs
mkdir workspace
cd workspace || exit
mv "${bam_file_path}" .
mv "${bambai_file_path}" .
outputdir="./out/samtool/count"
mkdir -p "${outputdir}"
samtools view -c "${bam_file_name}" "${regions[@]}" >> "${outputdir}/readcounts.txt"
counts_txt_id=$(dx upload "${outputdir}/readcounts.txt" --brief)
dx-jobutil-add-output counts_txt "${counts_txt_id}" --class=file
}
The main entry point triggers this subjob, providing the output of count_func as an input JBOR. This entry point gathers all the
readcount.txt files generated by the count_func jobs and sums the totals.This entry point returns
read_sum as a JBOR, which is then referenced as job output.sum_reads() {
set -e -x -o pipefail
echo "$filename"
echo "Value of read file array '${readfiles[@]}'"
dx-download-all-inputs
echo "Value of read file path array '${readfiles_path[@]}'"
echo "Summing values in files"
readsum=0
for read_f in "${readfiles_path[@]}"; do
temp=$(cat "$read_f")
readsum=$((readsum + temp))
done
echo "Total reads: ${readsum}" > "${filename}_counts.txt"
read_sum_id=$(dx upload "${filename}_counts.txt" --brief)
dx-jobutil-add-output read_sum "${read_sum_id}" --class=file
In the main function, the output is referenced
echo "Specifying output file"
dx-jobutil-add-output counts_txt "${countsfile_job}:read_sum" --class=jobref
}
Last modified 3yr ago