Problem with the name of Res.fasta and questions about replicons

Hi,

Thank you for developping this tool. It is really great to be able to annotate several elements in one command line. After running Bacant v3.4.0 on some genomes I have some comments and questions:

I suppose this is a typo in the output: annotaion.htlm. And that it should be annotation.htlm?
I downloaded the last database (v3.1) and when using this database (with the option -p), my outputs for resistance genes were all empty. I realized that in the version 3.1 the files are called Res.fasta.n instead of Res.n.. There was no error message though, intead the message said "AMR done", like if it worked fine. Would it be possible to add a checking for the db, in addition of the checking of the fasta file?
By the way, for replicons, the name of the file is replicon.fasta.n**, which is what is indeed read by bacant (no need to rename it contraty to Res.fasta).
If I am not mistaken, there is no mention of Replicons in the article Would it be possible to speak about them in the README? Would it be possible to have some information on that? Where does the database come from? What are the blast parameters (since we cannot set -c and -i on those) ? Is there anything else other than the blast done? I was also wondering whether it would be possible in a next version to add the replicons to the annotation.tsv?
And finally, would you have any advice on how to choose the -c and -i parameters?

Thank you

Hi,

It is a typo. we will change to annotation.html.
The database v3.4.0 harboured the different format with the previous database. we will detect the database version for the compatibility in the next version.
we will add the parameter and the introduction for replicon in the next version. The blast parameters is identity 90 coverage 60.

Best wishes,

Xiaoting

-----原始邮件----- 发件人:HeloiseMuller @.> 发送时间:2024-01-12 01:10:33 (星期五) 收件人: xthua/bacant @.> 抄送: Subscribed @.***> 主题: [xthua/bacant] Problem with the name of Res.fasta and questions about replicons & integrons (Issue #9)

Hi,

Thank you for developping this tool. It is really great to be able to annotate several elements in one command line. After running Bacant v3.4.0 on some genomes I have some comments and questions:

I suppose this is a typo in the output: annotaion.htlm. And that it should be annotation.htlm? I downloaded the last database (v3.1) and when using this database (with the option -p), my outputs for resistance genes were all empty. I realized that in the version 3.1 the files are called Res.fasta.n instead of Res.n.. There was no error message though, intead the message said "AMR done", like if it worked fine. Would it be possible to add a checking for the db, in addition of the checking of the fasta file? By the way, for replicons, the name of the file is replicon.fasta.n**, which is what is indeed read by bacant (no need to rename it contraty to Res.fasta). It seems that there are additional features since the publication, would it be possible to speak about them in the README? I am thinking about Replicons and Integrons. If I am not mistaken, there is no mention of Replicons in the article. Would it be possible to have some information on that? What are the blast parameters (since we cannot set -c and -i on those) ? Is there anything else other than the blast done? I was also wondering whether it would be possible in a next version to add them to the annotation.tsv? About Integrons, according to the article it uses the database INTEGRALL. But in the code I can see that Bacant also runs the tool IntegronFinder. I was thus condering how does Bacant deal with both methods? And finally, would you have any advice on how to choose the -c and -i parameters?

Thank you

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Xiaoting Hua, PhD, Associate Professor Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Qingchundong 3 RD, Hangzhou 310016, China

xthua / bacant

Problem with the name of Res.fasta and questions about replicons #9