想下载拟南芥一些特定组织的RNAseq数据,通过entrez把各个库的info下载,然后筛选后进行下载
Entrez Direct: E-utilities on the UNIX Command Line
Installation
cd ~
/bin/bash
perl -MNet::FTP -e \
'$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);
$ftp->login; $ftp->binary;
$ftp->get("/entrez/entrezdirect/edirect.tar.gz");'
gunzip -c edirect.tar.gz | tar xf -
rm edirect.tar.gz
builtin exit
export PATH=${PATH}:$HOME/edirect >& /dev/null || setenv PATH "${PATH}:$HOME/edirect"
./edirect/setup.sh
安装后报错:
FAILED TO DOWNLOAD:
xtract.UNSUPPORTED.gz (xtract.UNSUPPORTED.gz: No such file or directory)
gzip: xtract.UNSUPPORTED.gz: No such file or directory
Unable to download xtract executable.
FAILED TO DOWNLOAD:
rchive.UNSUPPORTED.gz (rchive.UNSUPPORTED.gz No such file or directory)
gzip: xtract.UNSUPPORTED.gz: No such file or directory
Unable to download rchive executable.
......
没管报错,直接执行
echo "export PATH=\${PATH}:/home/zorn/edirect" >> $HOME/.bashrc
执行我的搜索:
./esearch -db SRA -query "Arabidopsis thaliana[ORGN]" | efetch -db SRA -format runinfo -mode XML > out.csv