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jiwoongbio / VAMPr

VAriant Mapping and Prediction of antimicrobial resistance
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VAMPr

VAriant Mapping and Prediction of antimicrobial resistance

Requirements

  1. Perl - https://www.perl.org
  2. R - http://www.r-project.org
  3. Perl module Bio::DB::Fasta - https://metacpan.org/pod/Bio::DB::Fasta
  4. Perl module Statistics::R - https://metacpan.org/pod/Statistics::R
  5. R library caret - https://cran.r-project.org/web/packages/caret/index.html
  6. R library xgboost - https://cran.r-project.org/web/packages/xgboost/index.html
  7. DIAMOND - https://github.com/bbuchfink/diamond
  8. Linux commands: sort, wget - https://www.gnu.org/software/wget/

Install

If you already have Git (https://git-scm.com) installed, you can get the latest development version using Git. It will take a few seconds.

git clone https://github.com/jiwoongbio/VAMPr.git

Usages

Options: -h display this help message -t DIR directory for temporary files [$TMPDIR or /tmp] -C STR codon and translation e.g. ATG=M [NCBI genetic code 11 (Bacterial, Archaeal and Plant Plastid)] -S STR comma-separated start codons [GTG,ATG,CTG,TTG,ATA,ATC,ATT] -T STR comma-separated termination codons [TAG,TAA,TGA] -L INT minimum translation length [10] -p INT number of threads [1] -e FLOAT maximum e-value to report alignments [10] -c FLOAT minimum coverage [0.8] -s FILE output SAM file -a FILE output alignment file -A all variants


* VAMP_protein.pl

Usage: perl VAMP_protein.pl [options] protein.fasta > VAMP.txt

Options: -h display this help message -t DIR directory for temporary files [$TMPDIR or /tmp] -p INT number of threads [1] -e FLOAT maximum e-value to report alignments [10] -c FLOAT minimum coverage [0.8] -s FILE output SAM file -a FILE output alignment file -A all variants


* VAMP_database.pl

Usage: perl VAMP_database.pl [options] [KEGG_orthology.txt]

Options: -h display this help message -r redownload data -c FLOAT sequence identity threshold [0.7] -d decoy -a FILE additional protein sequence file including orthology, protein and sequence columns -p INT number of threads [1]


* VAMP_database.feature.pl

Usage: perl VAMP_database.feature.pl [options]

Options: -h display this help message -r redownload data


* VAMP_feature.pl

Usage: perl VAMP_feature.pl [options] VAMP.txt > VAMP_feature.txt

Options: -h display this help message


* VAMP_fisher.pl

Usage: perl VAMP_fisher.pl [options] phenotype=VAMP.txt[,...] [...] > VAMP_fisher.txt

Options: -h display this help message -g FILE genotype file -c cluster only -o orthology only


* VAMP_fisher.filter.pl

Usage: perl VAMP_fisher.filter.pl VAMP_fisher.txt > VAMP_fisher.filter.txt

Options: -h display this help message -a FLOAT alpha, p-value cutoff -D do not consider drive count -O do not consider odds ratio


* VAMP_model.pl

Usage: perl VAMP_model.pl [options] VAMP_model.RData phenotype=VAMP.txt[,...] [...]

Options: -h display this help message -g FILE genotype file -c cluster only -o orthology only -s INT seed [1] -f INT fold [5] -G STR grid


* VAMP_nestedCV.pl

Usage: perl VAMP_nestedCV.pl [options] VAMP_nestedCV.accuracy.txt phenotype=VAMP.txt,... [...]

Options: -h display this help message -g FILE genotype file -c cluster only -o orthology only -s INT seed [1] -f INT fold [5] -F INT outer fold [10] -G STR grid -i FILE image file


* VAMP_model.genotype.pl

Usage: perl VAMP_model.genotype.pl [options] VAMP_model.RData > VAMP_model.genotype.txt

Options: -h display this help message


* VAMP_predict.pl

Usage: perl VAMP_predict.pl [options] VAMP_model.RData [sample=]VAMP.txt [...]

Options: -h display this help message -c cluster only -o orthology only -p STR phenotype -i FILE image file


## Example

1. Download an example input genome FASTA file

wget --no-check-certificate https://cdc.biohpc.swmed.edu/VAMPr/example/Klebsiella_pneumoniae_MGH_43.fasta


2. Download VAMPr protein database

perl VAMP_database.pl


3. Identify AMR genotypes

perl VAMP.pl Klebsiella_pneumoniae_MGH_43.fasta > Klebsiella_pneumoniae_MGH_43.VAMP.txt


4. Download VAMPr prediction model

wget --no-check-certificate https://cdc.biohpc.swmed.edu/VAMPr/VAMP_model/573.amikacin.VAMP_model.RData wget --no-check-certificate https://cdc.biohpc.swmed.edu/VAMPr/VAMP_model/573.cefepime.VAMP_model.RData


5. Predict AMR phenotypes

perl VAMP_predict.pl 573.amikacin.VAMP_model.RData amikacin=Klebsiella_pneumoniae_MGH_43.VAMP.txt perl VAMP_predict.pl 573.cefepime.VAMP_model.RData cefepime=Klebsiella_pneumoniae_MGH_43.VAMP.txt