code for calculating mapped-read abundance for MAGs
1.make_cov_mp.py
Usage: generate MAG relative abundance table with multiprocessing
Options:
-h, --help show this help message and exit
-i INPUTF, --input=INPUTF
'*bam' data path
-f FASTA, --fasta=FASTA
contig fasta file
-o OUTPUTF, --output=OUTPUTF
coverage file name
-t WORKER, --threads=WORKER
working cpu number
-b BEDT, --bedtools=BEDT
bedtools absolute path
2.amr_mapped_range.py
Usage: get AMR coverage file from bamfiles
Options:
-h, --help show this help message and exit
-i INPUTF, --input=INPUTF
'*bam' data path
-a AMRFINDER, --amr=AMRFINDER
amrfinder result file folder
-o OUTPUTF, --output=OUTPUTF
coverage file name
-t WORKER, --threads=WORKER
working cpu number
-b BEDT, --bedtools=BEDT
bedtools absolute path
NMDS analysis in R
%%R
library(vegan)
dfMAG<-read.csv("output_from_code1",header=TRUE,row.names=1) %>% t()
bray_met<-vegdist(dfMAG,"bray")
df_bray<-as.matrix(bray_met)
# Perform NMDS
nmds_result <- metaMDS(df_bray, k = 2) # k is the number of dimensions
nmds_result