The donor of HGT predicted by HGTector-2.0b2

[Yliub]

@qiyunzhu Dear qiyuzhu;
I am liub, who talked with you in November last year.

I notice that you have updated some new funtion in the latest HGTector-2.0b2 version, but the moudle that predicted potential HGT donor at a specific phylogenetic rank is still unavailable. I try to realize the result by using HGTector-0.2.1 or 0.2.2 version. but it awalys show an error message or bug at different steps.
could please provide me with a solution to realize it in the HGTector-2.0b2 version, thanks a lot.

Regard
liub

[qiyunzhu]

@Yliub Thanks for waiting. I had some time to work out this feature. Here it is. You may upgrade HGTector by:

pip install -U git+https://github.com/DittmarLab/[email protected]

Then you can let the program report potential donors at a given rank (e.g., phylum) by:

hgtector analyze ... --donor-name --donor-rank phylum

The predicted HGT list files under hgts/ will now have this information.

I don't recommend specifying a low rank (such as "genus"), because in many scenarios HGT prediction cannot be this precise.

Hope this helps! Please let me know any thoughts.

[Yliub]

Dear qiyunzhu; Wish you everythings goes well, keeping continuous personal protection during the pandemic of COVID-2019! The latest release of HGTector2.0b3 received, and I am testing the feasibility using my own genomic data. Any questions will be feedback to you immediately after finishing running the program.Thank you very much with best regards Liub  

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------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "DittmarLab/HGTector" <[email protected]&gt;; 发送时间:&nbsp;2020年12月28日(星期一) 上午6:04 收件人:&nbsp;"DittmarLab/HGTector"<[email protected]&gt;; 抄送:&nbsp;"liub"<[email protected]&gt;;"Mention"<[email protected]&gt;; 主题:&nbsp;Re: [DittmarLab/HGTector] The donor of HGT predicted by HGTector-2.0b2 (#62) @Yliub Thanks for waiting. I had some time to work out this feature. Here it is. You may upgrade HGTector by: pip install -U git+https://github.com/DittmarLab/[email protected] Then you can let the program report potential donors at a given rank (e.g., phylum) by: hgtector analyze ... --donor-name --donor-rank phylum The predicted HGT list files under hgts/ will now have this information. I don't recommend specifying a low rank (such as "genus"), because in many scenarios HGT prediction cannot be this precise. Hope this helps! Please let me know any thoughts. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[Yliub]

Dear qiyunzhu; I have tested the latest version of HGTector2.0b3 using my own 30 bacterial genomic data. Among the 30 results, 29 results were credible, but the 30th genome was predicetd to contain 2038 genes originated from HGT envent, which i think was suspicious. Similar result was received by using the HGTector0.2.1 version. I have uploaded the 30th genome data and the predicted result to you. could you please help checking it？ with best regards Liub

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------------------ 原始邮件 ------------------ 发件人:"DittmarLab/HGTector"<[email protected]&gt;; 发送时间:2020年12月28日(星期一) 上午6:04 收件人:"DittmarLab/HGTector"<[email protected]&gt;; 抄送:"liub"<[email protected]&gt;;"Mention"<[email protected]&gt;; 主题:Re: [DittmarLab/HGTector] The donor of HGT predicted by HGTector-2.0b2 (#62) @Yliub Thanks for waiting. I had some time to work out this feature. Here it is. You may upgrade HGTector by: pip install -U git+https://github.com/DittmarLab/[email protected] Then you can let the program report potential donors at a given rank (e.g., phylum) by: hgtector analyze ... --donor-name --donor-rank phylum The predicted HGT list files under hgts/ will now have this information. I don't recommend specifying a low rank (such as "genus"), because in many scenarios HGT prediction cannot be this precise. Hope this helps! Please let me know any thoughts. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.