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Counting the number of species from NCBI Taxonomy browser

Hi, I need to count the number of species for each genus search from NCBI Taxonomy Browser result. Is there any way to do this using coding ? Manual counting is highly tedious work. Thanks

taxonomy ncbi
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updated by shenwei356 shenwei356 • written by adarsh • adarsh

1 answer

Try using taxonkit, but it needs some time.

There are 96645 TaxIds at genus rank.

$ time taxonkit list --ids 1 \
    | taxonkit filter --equal-to genus
    | wc -l
96645

Counting for 100 genuses costs: 

time taxonkit list --ids 1 \
    | taxonkit filter --equal-to genus \
    | head -n 100 \
    | rush 'echo -ne "{}\t$(echo {} \
                                | taxonkit list --ids {} \
                                | taxonkit filter --equal-to species \
                                | wc -l \
                            )\n" ' \
    | csvtk sort -H -t -k 2:nr \
    | head -n 5

190729  178
558016  157
558017  55
687331  40
1307798 32

real    1m11.472s
user    16m28.239s
sys     0m55.687s

It works but is not efficient for this work.

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written by shenwei356 shenwei356

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