Question: esearch problem downloading files
0
gravatar for cristina_sabiers
3.4 years ago by
Spain
cristina_sabiers70 wrote:

Hi all!

Long time...I got pretty bussy learning Pandas to work with dataframes in a decent way , just miss learn more deep python and unix comands....step by step

I try to do manually mapping virus like VIP pipeline just to learn how they do, the case is get stock at this step, on db_instaler.sh stands

 esearch -db nuccore -query "Viruses[Organism] NOT cellular organisms[ORGN] NOT wgs[PROP] NOT gbdiv syn[prop] AND (srcdb_refseq[PROP] OR nuccore genome samespecies[Filter])" | efetch -format fasta > all_virus.fna

Asume the code its for download virus sequences with esearch...Its the first time I install and use this utility

   cd ~
   perl -MNet::FTP -e \
   '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);
    $ftp->login; $ftp->binary;
     $ftp->get("/entrez/entrezdirect/edirect.tar.gz");'
    gunzip -c edirect.tar.gz | tar xf -
    rm edirect.tar.gz
    export PATH=$PATH:$HOME/edirect
    ./edirect/setup.sh

I open terminal and type the sample above or the one from VIP:

esearch -db protein -query "lycopene cyclase" | efetch -format fasta

and gives me the next asnwer:

You have requested a page which is not open to the public. Your request did not meet the criteria required to grant access to this page. If you believe that you are being denied access to the page in error, send an e-mail problem report to

virus • 1.1k views
ADD COMMENTlink modified 3.3 years ago by Istvan Albert ♦♦ 85k • written 3.4 years ago by cristina_sabiers70

I do something wrong? its like I go to restricted area?

Thanks for the help

ADD REPLYlink written 3.4 years ago by cristina_sabiers70
1

esearch -db protein -query "lycopene cyclase" | efetch -format fasta

I get the expected protein sequences. No errors.

ADD REPLYlink written 3.4 years ago by genomax92k

Thank genomax, must be st wrong in the installation or in some crazy way they bann me, will try in my other O.S

ADD REPLYlink written 3.4 years ago by cristina_sabiers70
2
gravatar for Istvan Albert
3.3 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

Your edirect is version is outdated.

When that happens it produces an extremely confusing errors where it blabbers about "access criteria" etc but in fact, the tool version does not match the site.

Update your edirect and you'll be fine. Or as I put it in my documenation:

# Perhaps you have a chronic case of Entrez Direct? Update it!
mkdir -p ~/src
curl ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip > ~/src/edirect.zip
unzip -o ~/src/edirect.zip  -d ~/src
echo 'export PATH=~/src/edirect:$PATH' >> ~/.bashrc
source  ~/.bashrc

then see the version:

efetch -version
7.00
ADD COMMENTlink written 3.3 years ago by Istvan Albert ♦♦ 85k

thank you so much! worked with your code.

Thanks

ADD REPLYlink written 3.3 years ago by cristina_sabiers70
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