AmrPlusPlus_SNP

Introduction

The AMRPlusPlus_SNP repository contains multiple progams used to either extract SNP info or to verify ARGs for resistant-conferring SNPs.

SNP_Verification Installation Instructions

For Mac and Linux

If not already done so, install latest version of Python3 and of the pysam and pandas modules
Open terminal
Install the AMRPlusPlus_SNP repo by typing gh repo clone https://github.com/Isabella136/AmrPlusPlus_SNP
Run the SNP_Verification.py program by typing python3 SNP_Verification.py

For Windows

Currently, pysam is difficult to install on Windows, therefore it is recommended to instead use a linux environment via command prompt to run the SNP_Verification program

List of Arguments

-a: amrplusplus; is either true or false
-c: config file; if this argument is used, must be the first listed
-h: help
-i: input file
-l: license disclaimer
-o: output folder
-r: conditions for redistribution

--mt_and_wt: true by default, used in case of insertion leading to presence of both mt and wt; if true, mark as resistant; if false, mark as susceptible
--detailed_output: false by default, determines whether a more detailed output will be given; can be either false, 'all', or include a list of accessions seperated by commas
--count_matrix: count matrix that will be updated if amrplusplus is true
--count_matrix_final: the file where the updated count matrix will be found if amrplusplus is true

Lists of Folders in Main

data Folder

Contains all SNP information extracted from SNPInfoExtraction (see in-depth branch), the megares database, and sample input/output.

InfoExtraction Folder

Contains the following three folders:

KargvaInfoExtraction Folder

Contains the KargvaInfoExtracion program that extracts SNP information retrieved from the database in the KARGVA repository and saves it in the extracted_SNP_files folder.

LiteratureInfoExtraction Folder

Contains the LiteratureInfoExtracion program that extracts SNP information retrieved from the literature (which was previously compiled into the "SNPinfo_literature.csv" file) and saves it in the extracted_SNP_files folder.

MetamarcInfoExtraction Folder

Contains the MetamarcInfoExtraction program that extracts SNP information retrieved from the database in the MetaMARC repository and saves it in the extracted_SNP_files folder.
Also contains the metamarc_files folder which includes the folowing files:

"mmarc_model_members.csv": lists mmarc models and corresponding ARGs; ARGs are represented by their MEGARes v1 database header
"mmarc_snpsearch_metadata2.txt": lists of SNP information for each mmarc model
"mmarc_snpsearch_metadata2_modified.txt": another version of the previous text file that has been modified for use by the MetamarcInfoExtraction program

mapping_files Folder

Contains two csv files: the first file is used to map the MEGARes v1 database headers (used by MetaMARC) to headers used by external databases, and the second file is used to map the MEGARes v2 database headers (used by AMRPlusPlus_SNP) to headers used by external databases.

SNP_Verification_Process and SNP_Verification_Tools Folder

Contains the SNP_Verification program that verifies SAM files for resistance-conferring SNPs.
Uses all of the SNP information saved in the data folder.

Isabella136 / AmrPlusPlus_SNP

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