How to compare one single genome A with multiple genomes(n>50)?

hoelzer / pocp

Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.

GNU General Public License v3.0

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How to compare one single genome A with multiple genomes(n>50)? #2

Closed liuqian666 closed 4 years ago

liuqian666 commented 4 years ago

Hello! I have one genome A and many reference genomes (download from Genbank), and the number of reference genomes is 110. If I do the command './pocp.rb example/ example/results/ 2', it will take too much time to compare with each other. So, do you know how to adjust the command to solve the problem? Thank you very much!

hoelzer commented 4 years ago

Hi! Ah okay, so you don't want to do a pairwise all-vs-all comparison.

Let me check, I think this should be doable with some small change.

best

hoelzer commented 4 years ago

@liuqian666 srry for the late reply, I just found some time to look into this.

cd pocp
git pull origin master
./pocp.rb example/ example/results/ 2 Cav_10DC88.faa

should be the job now.

Please let me know if this solves your issue so I can close this and do another release of the code.

Thanks, Martin

liuqian666 commented 4 years ago

Thank you very much! It helps me a lot !

hoelzer commented 4 years ago

Great, i will close this issue and generate a new release with this feature. Let me know if something else is needed

hoelzer commented 4 years ago

https://github.com/hoelzer/pocp/releases/tag/1.1.1