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linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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run_dbcan hotpep output contains non-existent EC numbers #81

Closed Rob-murphys closed 2 years ago

Rob-murphys commented 2 years ago

The hotpep.out for run_dbcan contains non-existent EC numbers that seems to be a merging of multiple EC numbers, for example 3.2.1.13.2.1 which can be seen in the attached output. This seems to be a combination of 3.2.1.1 and 3.2.1.- with the .- omitted.

Hotpep.zip

linnabrown commented 2 years ago

We are updating the new version that removing Hotpep and adding eCAMI which can also look for the subfamily. You can try the new software instead. Thank you so much and happy holiday.

Rob-murphys commented 2 years ago

Oh cool! How come you are stopping the use of hotpep?

yinlabniu commented 2 years ago

We have developed a better tool called eCAMI. Others also found that hotpep's performance is not very good: https://doi.org/10.6084/m9.figshare.14370836.v1

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Oh cool! How come you are stopping the use of hotpep?

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Rob-murphys commented 2 years ago

Very cool stuff!! Is there an ETA on the release?

linnabrown commented 2 years ago

I have already updated just now. Please check the github. Also, since eCAMI could not integrated in PYPI so you had to git clone https://github.com/linnabrown/run_dbcan.git and eCAMI is integrated inside run_dbcan folder. And don't forget to pip install run_dbcan=3.0.2 to update

Rob-murphys commented 2 years ago

Many thanks, i will try this ASAP! So it is able to get the EC level resolution similar to Hotpep right?

yinlabniu commented 2 years ago

That's right. Even better is that the overview file now contains a column named EC numbers (extracted from eCAMI).

From: Lamm-a @.> Sent: Monday, December 20, 2021 1:58 PM To: linnabrown/run_dbcan @.> Cc: Yanbin Yin @.>; Comment @.> Subject: Re: [linnabrown/run_dbcan] run_dbcan hotpep output contains non-existent EC numbers (Issue #81)

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Many thanks, i will try this ASAP! So it is able to get the EC level resolution similar to Hotpep right?

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Rob-murphys commented 2 years ago

I can't express enough how cool and thankful I am you have done this! You guys do awesome work :)

linnabrown commented 2 years ago

Thank you.