123456789101112131415161718192021222324252627282930313233343536 |
- #!/bin/bash
- create_test_cool(){
- url=$1
- outpath=$2
- binsize=$3
- if [[ -f ${outpath}/test.cool ]]; then return; fi
- if [[ ! -f ${outpath}/source.pairs.gz ]]
- then
- echo "[Error] Please manually download the file ${url} to ${outpath}"
- echo " and give it source.pairs.gz as name"
- exit -1
- fi
- zcat ${outpath}/source.pairs.gz | head -26 | tail -2 | cut -d' ' --output-delimiter=$'\t' -f 2,3 > ${outpath}/test.chrom.sizes
- cooler cload pairs --chrom1 2 --pos1 3 --chrom2 4 --pos2 5 \
- ${outpath}/test.chrom.sizes:${binsize} \
- ${outpath}/source.pairs.gz \
- ${outpath}/test.cool
- rm ${outpath}/source.pairs.gz
- cooler balance --force --max-iters 1000 ${outpath}/test.cool
- }
- test_data_path="tests/testthat/data"
- mkdir -p ${test_data_path}
- # Test cool file
- source_cool_file="https://data.4dnucleome.org/files-processed/4DNFI2EK1IOQ/@@download/4DNFI2EK1IOQ.pairs.gz"
- test_cool_binsize=50000
- create_test_cool ${source_cool_file} ${test_data_path} ${test_cool_binsize}
|