maricultureMAGs

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