ncbi_acc2gtdb_acc

Mapping NCBI genbank accession to GTDB accession

Strategy

# genbank assembly
NCBI assembly_accession (1) <- (1) ftp-url/fna.gz (1) <- (n) NCBI accession

# gtdb
NCBI assembly_accession (1) -> (1) GTDB accession

Tools

• csvtk
• rush

Steps

# -------------- download meta data -----------------

# download assembly summary files
wget -c https://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/assembly_summary.txt -O as-genbank-archaea.txt
wget -c https://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt -O as-genbank-bacteria.txt 

# download gtdb metadata
wget -c https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/95.0/ar122_metadata_r95.tar.gz
wget -c https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/95.0/bac120_metadata_r95.tar.gz 
   

# -------------- preparation -----------------

# convert assembly summary files to TSV
for f in as-*.txt; do 
    sed 1d $f | sed "1s/^# //" | sed "s/\"/$/g" > ${f%.*}.tsv
done


# concatenate gtdb metadata, and extract gets
#     ncbi_genbank_assembly_accession ->  gtdb accession
tar -zxvf ar122_metadata_r95.tar.gz
tar -zxvf bac120_metadata_r95.tar.gz        
cat ar122_metadata_r95.tsv <(sed 1d bac120_metadata_r95.tsv) \
    | csvtk cut -t -f ncbi_genbank_assembly_accession,accession \
    | csvtk replace -t -f ncbi_genbank_assembly_accession -p "\.\d+$" \
    | sed 1d \
    > ncbi_ass2gtdb_acc.tsv
    
# extract NCBI assembly_accession and ftp path
cat as-genbank-archaea.tsv <(sed 1d as-genbank-bacteria.tsv) \
    | csvtk cut -t -f assembly_accession,ftp_path \
    | csvtk replace -t -f assembly_accession -p "\.\d+$" \
    | csvtk uniq -t -f assembly_accession \
    > ncbi_ass2ftp.tsv

# filter these in gtdb
cat ncbi_ass2ftp.tsv \
    | sed 1d \
    | csvtk grep -H -t -f 1 -P <(cut -f 1 ncbi_ass2gtdb_acc.tsv) \
    > ncbi_ass2ftp.filter.tsv

# counting
wc -l ncbi_ass2gtdb_acc.tsv ncbi_ass2ftp.filter.tsv
# 194600 ncbi_ass2gtdb_acc.tsv
# 194436 ncbi_ass2ftp.filter.tsv

# find out these not in genbank.
# possible reasson: deleted fro genbank, e.g., GCA_007036345
cat ncbi_ass2gtdb_acc.tsv \
    | csvtk grep -H -t -f 1 -v -P <(cut -f 1 ncbi_ass2ftp.tsv) \
    | cut -f 1 \
    > ncbi_ass2gtdb_acc.tsv.not-in-sa.tsv 


# -------------- mapping NCBI accession to NCBI assembly_accession -----------------

# parse all genomes, extract accession, and append NCBI assembly_accession.
# it may report "gzip: stdin: unexpected end of file",
# may be due to my bad internet connection.
#
# time: abount 10 hours with a VPS at San Francisco, CA
threads=20
time cat ncbi_ass2ftp.filter.tsv \
    | csvtk replace -H -t -f 2 -p "^ftp" -r "https" \
    | rush -k -j $threads 'wget {2}/{2%}_genomic.fna.gz -o /dev/null -O - \
        | gzip -cd | grep "^>" | cut -f 1 | sed "s/>//" | awk "{print \$1, \"{1}\"}"' \
    | sed 's/ /\t/' \
    | gzip -c \
    > ncbi_acc2ncbi_ass.tsv.gz
    
# -------------- mapping NCBI accession to GTDB accession -----------------

csvtk replace -H -t -f 2 -p '(.+)' -r '{kv}' --key-miss-repl __ \
    -k ncbi_ass2gtdb_acc.tsv ncbi_acc2ncbi_ass.tsv.gz \
    | gzip -c \
    > ncbi_acc2gtdb_acc.tsv.gz

Result

stats

# records of gtdb
echo "records of GTDB: $(cat ncbi_ass2gtdb_acc.tsv | wc -l)"
# without genbank assebmly assembly_accession
echo "    these without assembly_accession: $(cat ncbi_ass2gtdb_acc.tsv | grep -c none)"    
# these in genbank
echo "    these available in current GenBank: $(cat ncbi_ass2ftp.filter.tsv | wc -l)"
# actually downloaded
echo "    actually downloaded: $(zcat ncbi_acc2gtdb_acc.tsv.gz | cut -f 2 | uniq | wc -l)"

records of GTDB: 194600
    these without assembly_accession: 7
    these available in current GenBank: 194436
    actually downloaded: 194431

preview

zcat ncbi_acc2gtdb_acc.tsv.gz | head -n 5
LMVM01000001.1  RS_GCF_002287175.1
LMVM01000002.1  RS_GCF_002287175.1
LMVM01000003.1  RS_GCF_002287175.1
LMVM01000004.1  RS_GCF_002287175.1
LMVM01000005.1  RS_GCF_002287175.1