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PATRIC3 / patric3_website

Legacy PATRIC Website (JBoss Portal Version)
MIT License
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Naming Metagenome Bins #2053

Open Tinyman392 opened 6 years ago

Tinyman392 commented 6 years ago

If I were to bin 2 metagenomes that both contain an E. coli clonal population (along with other stuff). Both metagenomes would return a genome named Escherichia coli clonal population. It may be useful to allow users to add some unique identifier to the end of each of the meta genome clonal population names similar to what we do for annotation since these names can't be changed after the fact.

See the last two genomes in the following screenshot.

screen shot 2018-07-27 at 10 25 33 am
bparrello commented 5 years ago

I can add the sample ID "clonal population from SRS011132" if that would help.

Tinyman392 commented 5 years ago

I can add the sample ID "clonal population from SRS011132" if that would help.

That would help, though it would be useful to be able to determine what SRS011132 is.

bparrello commented 5 years ago

I have added a parameter to the main binning script to allow the invoker to specify the genome name suffix (the default remains "clonal population"). We can use it in the future to give (for example) the user the ability to specify the names.

Tinyman392 commented 5 years ago

Is this just on the CLI or on the website as well? I can’t seem to find it on the website, I’ve filled out both the Output Name and Genome Group Name and neither of them seem to change the genome name.

bparrello commented 5 years ago

All I did was update the underlying software. Bob and the crew need to decide how they want to utilize it and what user updates are needed; then they need to install it. I don’t expect any of that to happen until after the next release, though.

Tinyman392 commented 5 years ago

Ok, thanks Bruce, just confirming that it wasn't live on the website yet.