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- #!/bin/bash
- set -euo pipefail
- fgbio_cmd="java -Xmx8G -jar /Users/nhomer/git/fg/fgbio/target/scala-2.12/fgbio-0.8.0.jar"
- function build_it ()
- {
- local src_build=$1;
- local target_build=$2;
- pushd ../${target_build}
- if [ ! -f ${src_build}_to_${target_build}_mapping.txt ]; then
- $fgbio_cmd CollectAlternateContigNames \
- -i ../${src_build}/${src_build}.assembly_report.txt \
- -o ${src_build}_to_${target_build}_mapping.txt \
- -p RefSeqAccession \
- -a UcscName \
- -s AssembledMolecule UnlocalizedScaffold UnplacedScaffold;
- fi
- if [ ! -f ${target_build}.alt_names.txt ]; then
- $fgbio_cmd CollectAlternateContigNames \
- -i ../${src_build}/${src_build}.assembly_report.txt \
- -o /dev/stdout \
- -p RefSeqAccession \
- -a UcscName GenBankAccession \
- -s AssembledMolecule UnlocalizedScaffold UnplacedScaffold \
- --by-line \
- | awk '{print $2, $1; print $2, $3;}' \
- > ${target_build}.alt_names.txt
- fi
- if [ ! -f ${target_build}.gff.gz ]; then
- $fgbio_cmd UpdateGffContigNames \
- -i ../${src_build}/${src_build}.gff.gz \
- -a ${src_build}_to_${target_build}_mapping.txt \
- -o ${target_build}.gff.gz \
- --skip-missing
- fi
- if [ ! -f ${target_build}.fasta ]; then
- $fgbio_cmd UpdateFastaNames \
- -i ../${src_build}/${src_build}.fasta \
- -a ${src_build}_to_${target_build}_mapping.txt \
- -o ${target_build}.fasta \
- --skip-missing
- fi
- if [ ! -f ${target_build}.fasta.fai ]; then
- samtools faidx ${target_build}.fasta
- fi
- if [ ! -f ${target_build}.dict ]; then
- java -Xmx8G -jar /Users/nhomer/git/picard/build/libs/picard.jar \
- CreateSequenceDictionary \
- R=${target_build}.fasta \
- O=${target_build}.dict \
- AS=${target_build} \
- URI=ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_${src_build}/GCF_000001405.25_${src_build}_genomic.fna.gz \
- SP="Homo sapiens" \
- AN=${target_build}.alt_names.txt;
- fi
- if [ ! -f ${target_build}.fasta.pac ]; then
- bwa index ${target_build}.fasta;
- fi
- popd
- }
- build_it GRCh37.p13 hg19
- build_it GRCh38.p12 hg38
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