build_alt_files.sh

#!/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 \
            --single-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 \
            -m ${src_build}_to_${target_build}_mapping.txt \
            -o ${target_build}.gff.gz \
            --skip-missing
    fi
    if [ ! -f ${target_build}.fasta ]; then
        $fgbio_cmd UpdateFastaContigNames \
            -i ../${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