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widdowquinn / pyani

Application and Python module for average nucleotide identity analyses of microbes.
http://widdowquinn.github.io/pyani/
MIT License
185 stars 54 forks source link

How do I provide a labels.txt or classes.txt file? #394

Closed widdowquinn closed 1 year ago

widdowquinn commented 2 years ago

From #393

Hi, can you please tell me how to give lable.txt and class.txt file for those genome which are not downloaded by pyani download option ..i mean i want to label ani result but i don't have this two files because i had already downloaded data.

widdowquinn commented 2 years ago

The quickest way to do this in v0.3 is to use the pyani index command.

As you (@neelam19051) are using v0.2 you'll hae to construct your labels.txt and classes.txt files manually. Spreadsheet software like Excel or Google Sheets might be useful for you.

In v0.2, your labels file should resemble this:

NC_002696   C.crescentus CB15
NC_014100   C.segnis ATCC 21756
NC_011916   C.crescentus NA1000
NC_010338   Caulobacter sp. K31

and the classes file this:

NC_002696   C. crescentus
NC_014100   2
NC_011916   C. crescentus
NC_010338   3

The first column is the filestem for the sequence file, and the second column is the label or class in each case. The columns are separated by a tab character.

neelam19051 commented 2 years ago

Hi, How to classify strain of same species for classes.txt file and how to intrepret ANI result? . i don't see here any link for attachment so can i mail to you?

widdowquinn commented 2 years ago

Hi @neelam19051

How to classify strain of same species for classes.txt file and how to intrepret ANI result? . i don't see here any link for attachment so can i mail to you?

For questions unrelated to the original topic in the header, please open a new issue.

How to classify bacteria as the same or different species is an open scientific question, and there is no single correct answer that is accepted by everyone. I have opinions on the topic, but I recommend that you start with the relevant literature for your organism, e.g.

or for the topic in general, e.g.

We have documentation for v0.3 describing basic interpretation of pyani output, and where the plots are similar to those produced by v0.2, the interpretation is the same.

L.