duplicate taxid from name2taxid

[slaperriere]

Hello,

I am getting duplicate values from name2taxid when running

taxonkit name2taxid -i 2 filename

My input:
ESP_3 Bacteria
ESP_84 Bacteria
ESP_136 Bacteria
ESP_149 Bacteria
ESP_166 Bacteria
ESP_169 Bacteria
ESP_181 Bacteria
ESP_187 Bacteria
ESP_196 Bacteria

Output:
ESP_3 Bacteria 2
ESP_3 Bacteria 629395
ESP_84 Bacteria 2
ESP_84 Bacteria 629395
ESP_136 Bacteria 2
ESP_136 Bacteria 629395
ESP_149 Bacteria 2
ESP_149 Bacteria 629395
ESP_166 Bacteria 2
ESP_166 Bacteria 629395

Some lines as seen above are duplicated with a different taxid. There are no duplicates in the input.

Do you you what could be causing this?

Thank you!

[shenwei356]

Thanks for reporting this.

taxonkit name2taxid searches both scientific name and synonym, 629395 has a synonym of Bacteria...

629395  |       Bacteria        |       Bacteria <stick insect> |       synonym |
629395  |       Bacteria Latreille et al. 1825  |               |       scientific name |
629395  |       Bacteria Latreille, Peletier de Saint Fargeau, Serville & Guerin, 1825  |               |       authority       |
629395  |       Bacteria stick insect   |               |       common name     |

A new flag -s/--sci-name added for only searching scientific name:

• taxonkit_darwin_amd64.tar.gz
• taxonkit_linux_amd64.tar.gz
• taxonkit_windows_amd64.exe.tar.gz

[slaperriere]

Great, thank you! It looks like it solved most of the problem.

However, I am still get some duplicates. Some examples are

ESP_48538 Paracoccus 265
ESP_48538 Paracoccus 249411
ESP_764 Actinobacteria 1760
ESP_764 Actinobacteria 201174
ESP_17204 Vertebrata 7742
ESP_17204 Vertebrata 1261581

[shenwei356]

it's not a bug, if you have switched on -s. Some taxids indeed share same scientific names, you can check their lineage. For these, I duplicate these lines, you may deduplicate them using awk or csvtk, or I can add a new flag.

[shenwei356]

@slaperriere Can I close this issue?

[slaperriere]

Yes. Thank you for your help!