metadownload 0.1.3

python mlst analysis tool

metadownload

此脚本为下载NCBI中biosample相关字段信息的python脚本

Installation

pip3 install metadownload

Dependency

• E-utilities

you should add E-utilities in your PATH

E-utilities install:

sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"

sh -c "$(wget -q ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh -O -)"

Usage

usage: metadownload -list <biosample_acc_list> -outdir <output>

Author: Qingpo Cui(SZQ Lab, China Agricultural University)

optional arguments:
  -h, --help      show this help message and exit
  -list LIST      <file>: biosample_acc_list, one accession per line
  -outdir OUTDIR  <path>: output directory name
  -v, --version   Display version

Output

You will get text file contains metainfo for each biosample accession named with the accession number and a csv format summary file