信阳建设企业网站公司,凡科做网站视频,长沙旅游必去的八个景点,手机网页版微信官网为了程序运行的便利性#xff0c;不想将Decontam放到windows的Rstudio里面运行#xff0c;需要直接在Ubuntu中运行#xff0c;并且为了在Decontam时进行其他操作#xff0c;使用python去运行R 首先你需要有一个conda环境#xff0c;安装了R#xff0c;Decontam#xff0…为了程序运行的便利性不想将Decontam放到windows的Rstudio里面运行需要直接在Ubuntu中运行并且为了在Decontam时进行其他操作使用python去运行R 首先你需要有一个conda环境安装了RDecontamphyloseqrpy2
mamba create -c bioconda -c conda-forge -p {os.path.join(args[conda_env_dir], LBSWrap-Decontam)} r-base4.3.1 python3.10 -y /dev/null 21
mamba install -p {os.path.join(args[conda_env_dir], LBSWrap-Decontam)} bioconda::bioconductor-decontam -y /dev/null 21
mamba install -p {os.path.join(args[conda_env_dir], LBSWrap-Decontam)} bioconda::bioconductor-phyloseq -y /dev/null 21
mamba install -p {os.path.join(args[conda_env_dir], LBSWrap-Decontam)} biopython -y /dev/null 21
os.path.join(args[conda_env_dir], LBSWrap-Decontam, pip)} install rpy2 /dev/null 21
然后建立这个python文件chmod 755给权限就行了
需要有你的fasta文件用于输出通过过滤的和未通过过滤的fasta序列otu文件metadata文件
#! /usr/bin/env python
#########################################################
# run Decontam (methodprevalence) in Ubuntu through python
# written by PeiZhong in IFR of CAASimport argparse
import rpy2.robjects as robjects
from Bio import SeqIO
import osparser argparse.ArgumentParser(descriptionrun Decontam (methodprevalence) in Ubuntu through python)
parser.add_argument(--otu_txt, -otu, typestr, requiredTrue, help OTU table file )
parser.add_argument(--metadata_txt, -metadata, requiredTrue, typestr, help Metadata file )
parser.add_argument(--way, -w, typestr, requiredTrue, help choice from isNotContaminant or isContaminant )
parser.add_argument(--threshold, -t, typefloat, defaultNone, help Threshold , isNotContaminant default 0.5, isContaminant default 0.1 )
parser.add_argument(--result_txt, -r, typestr, requiredTrue, help result txt from Decontam )
parser.add_argument(--input_fasta, -ifa, typestr, requiredTrue, help your fasta file )
parser.add_argument(--output_fasta, -ofa, typestr, requiredTrue, help clean fasta according to the result of Decontam )
parser.add_argument(--contamination_fasta, -cfa, typestr, requiredTrue, help contamination fasta according to the result of Decontam )args parser.parse_args()for filepath in [args.otu_txt, args.metadata_txt, args.input_fasta]:if not os.path.exists(filepath):raise FileNotFoundError(fThe file {filepath} does not exist.)if args.way not in [isNotContaminant, isContaminant]:raise ValueError(The way parameter must be either isNotContaminant or isContaminant.)if args.threshold is None:args.threshold 0.5 if args.way isNotContaminant else 0.1shi, fou (TRUE, FALSE) if args.way isNotContaminant else (FALSE, TRUE)r_code f
library(ggplot2)
library(decontam)
library(phyloseq)otu - read.table({args.otu_txt}, headerTRUE, row.names 1)
sample - read.table({args.metadata_txt}, headerTRUE, row.names 1)otu_table - otu_table(t(otu), taxa_are_rows FALSE)
sample_data - sample_data(sample)
ps - phyloseq(otu_table, sample_data)sample_data(ps)$is.neg - sample_data(ps)$Sample_or_Control Control
contamdf.notcontam - {args.way}(ps, methodprevalence, negis.neg, threshold{args.threshold},detailTRUE) # isNotContaminant - True means non-contaminants
write.table(contamdf.notcontam, file{args.result_txt}, sep\t, quoteF, row.namesT)robjects.r(r_code)df, df_contam {}, {}
with open(args.result_txt,r) as read_result:for line in read_result.readlines():if p.prev not in line and len(line.split(\t)) 6:name, determine line.split(\t)[0].strip(\n), line.split(\t)[6].strip(\n)if determine shi:df[name] 0elif determine fou:df_contam[name] 0with open(args.input_fasta, r) as fasta_file:sequences SeqIO.to_dict(SeqIO.parse(fasta_file, fasta))clean_sequences {key: sequences[key] for key in df}
contaminated_sequences {key: sequences[key] for key in df_contam}with open(args.output_fasta, w) as clean_file, open(args.contamination_fasta, w) as contaminated_file:SeqIO.write(clean_sequences.values(), clean_file, fasta)SeqIO.write(contaminated_sequences.values(), contaminated_file, fasta)
OTU示例和metadata示例参考....emmm算了比较麻烦我给你们看我的文件
注意R里面-这个横杠会被识别为.容易出错 使用示例
/home/zhongpei/hard_disk_sda2/zhongpei/Software/my_script/Decontam.py -t 0.5 \
-otu ${zubie}_${ruanjian}_decontam_pre.txt -metadata ${zubie}_metadata.txt \-w isContaminant -r ${zubie}_${ruanjian}_decontam.report \
-ifa ${zubie}_${ruanjian}_all.fa -ofa ${zubie}_${ruanjian}_decontam.fa \
-cfa ${zubie}_${ruanjian}_notgood.fa
