search

bhattlab / phanta

Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
MIT License
60 stars 9 forks source link

The question of Refseq id #25

Closed wen1112 closed 1 year ago

wen1112 commented 1 year ago

Hi, I have a question with RefSeq id, for example, the Phanta result provide a id "Faecalibacterium virus Mushu", but the file which you provided last time (Refseq_viruses_added.txt), the species id is "Faecalibacterium phage FP_Mushu", I want to find them the NCBI accession (NC_047913.1), and I met so many times such as this situations. Because the most time I have to search it one by one, instead of use a script to do it directly. So I want to know if there has a table for such a relate infornation?

For example: Phanta result --> Refseq_viruses_added.txt result Faecalibacterium virus Mushu --> Faecalibacterium phage FP_Mushu Klebsiella virus ST147VIM1phi7-1 --> Klebsiella phage ST147-VIM1phi7.1

yipinto commented 1 year ago

Hi! Phanta reports the species level as it appears in ncbi taxonomy. For example this is the species level name. Also see the subtree with Faecalibacterium phage FP_Mushu is "no rank" under Mushuvirus mushu. Anyhow, since names can change in the taxonomy anyway I recommend using the taxonomic ID to have that information.

wen1112 commented 1 year ago

Thank you for your responed