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Isabella136 / AmrPlusPlus_SNP

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File "SNP_Verification.py", line 275 #32

Open erazzolini opened 5 months ago

erazzolini commented 5 months ago

Hello Isabella,

I'm writing to you because I have a few problems to install Amr++_SNP.

I mannaged to install in a python 3.12 version and didn't work because of pysam and a problem with wheel. Than, I create a new environment with python 3.6, everything worked well but when I tried to install Amr++_SNP I received the followed problem:

(p36) [emanuelr@sgi ~/AmrPlusPlus_SNP]$ python3 SNP_Verification.py File "SNP_Verification.py", line 275 with (open(config['FULL_FILE_NAMES']['NTYPE_OUTPUT'], "w") as outputN, ^ SyntaxError: invalid syntax

Do you know what wrong I did?

Isabella136 commented 5 months ago

Amr++_SNP is only compatible with python 3.9+

Jingle-H commented 2 months ago

Hello Isabella,

I'm writing to you because I have some questions about the SNPinfo.csv.

I can not find the specific information of SNPs about some gene ids in the output file of the Amr++ pipeline (-snp Y) in this csv file. For example, MEG_8447 and MEG_1612.

Do you know the reason?

Thanks very much!

Isabella136 commented 2 months ago

In general, if a gene is not in SNPinfo.csv, it would be because those genes either don't need any SNPs or indels, or the SNPs/indels were not found in literature back when MEGARes 3.0 was published

Jingle-H commented 2 months ago

Thanks for the reply!

I would like to know why add the label "RequiresSNPConfirmation" to some genes if the information of their SNPs was not found in the literature, because this label was also added to the genes that have specific SNP information in SNPinfo.csv.

Isabella136 commented 2 months ago

I think you should contact Enrique Doster from Texas A&M since he is mostly in charge with maintaining the actual database