Download files from NCBI Assembly

Strain info

cat ~/.nwr/assembly_summary_refseq.txt |
    sed '1d' |
    tva stats -H --missing-count infraspecific_name,isolate,biosample |
    tva to md --fmt

# infraspecific_name
cat ~/.nwr/assembly_summary_refseq.txt |
    sed '1d' |
    tva select -H -f infraspecific_name |
    perl -nla -F"=" -e 'print $F[0]' |
    tva keep-header -- sort |
    uniq -c
#       1 infraspecific_name
#      38 breed
#     109 cultivar
#      82 ecotype
#   67134 na
#  456330 strain

cat ~/.nwr/assembly_summary_genbank.txt |
    sed '1d' |
    tva select -H -f infraspecific_name |
    perl -nla -F"=" -e 'print $F[0]' |
    tva keep-header -- sort |
    uniq -c
#       1 infraspecific_name
#     565 breed
#    2587 cultivar
#    1098 ecotype
# 1264802 na
# 2151541 strain

cat ~/.nwr/assembly_summary_refseq.txt ~/.nwr/assembly_summary_genbank.txt |
    grep -v "^#" |
    tva select -f 9 | # infraspecific_name
    perl -nla -F"=" -e 'print $F[1]' |
    tva keep-header -- sort |
    uniq -c |
    sort -nr |
    head
# 1331958
#    3722 GPSC3
#    2491 Human
#    2451 clinical isolate of L. monocytogenes
#    2360 MSSA
#    1612 ExPEC
#    1377 MRSA
#    1285 GPSC12
#     898 GPSC16
#     854 GPSC55

# String length
cat ~/.nwr/assembly_summary_refseq.txt |
    sed '1d' |
    tva select -H -f organism_name,infraspecific_name,asm_name,ftp_path |
    sed '1d' |
    perl -nla -F"\t" -e 'print join qq(\t), map {length} @F ;' |
    tva stats --exclude-missing --max 1,2,3,4
#91      88      92      166

Reference genomes

cd ~/Scripts/nwr/docs/

nwr member Bacteria Archaea -r family |
    grep -v -i "Candidatus " |
    grep -v -i "candidate " |
    grep -v " sp." |
    grep -v " spp." |
    sed '1d' |
    sort -n -k1,1 \
    > family.list.tsv

wc -l family.list.tsv
#707 family.list.tsv

FAMILY=$(
    cat family.list.tsv |
        cut -f 1 |
        tr "\n" "," |
        sed 's/,$//'
)

echo "
.headers ON
    SELECT
        *
    FROM ar
    WHERE 1=1
        AND family_id IN ($FAMILY)
        AND refseq_category IN ('reference genome')
    " |
    sqlite3 -tabs ~/.nwr/ar_refseq.sqlite \
    > reference.tsv

cat reference.tsv |
    tsv-select -H -f organism_name,species,genus,ftp_path,assembly_level \
    > raw.tsv

cat raw.tsv |
    grep -v '^#' |
    rgr dedup stdin |
    perl ~/Scripts/withncbi/taxon/abbr_name.pl -c "1,2,3" -s '\t' -m 3 --shortsub |
    (echo -e '#name\tftp_path\torganism\tassembly_level' && cat ) |
    perl -nl -a -F"," -e '
        BEGIN{my %seen};
        /^#/ and print and next;
        /^organism_name/i and next;
        $seen{$F[3]}++; # ftp_path
        $seen{$F[3]} > 1 and next;
        $seen{$F[5]}++; # abbr_name
        $seen{$F[5]} > 1 and next;
        printf qq{%s\t%s\t%s\t%s\n}, $F[5], $F[3], $F[1], $F[4];
        ' |
    keep-header -- sort -k3,3 -k1,1 \
    > Bacteria.assembly.tsv

File format: .assembly.tsv

A TAB-delimited file for downloading assembly files.