Perl/Python script for batch download mRNA sequences for multiple genes

Question

[Shicheng Guo]

Hi All,

I hope to find a perl/python script for the multiple gene mRNA/transcript sequence (fasta) download which take Gene Symbol as input. for example, I want to download mRNA sequences for PADI1, PADI2, PADI3, PADI4, PADI5,PADI6 at same time and output a fasta file.

Thanks.

[GenoMax]

• You can use NCBI unix utils and a loop to go through your gene ID's.
• You can use Ensembl REST (or Perl) API

Answer 1

[Carambakaracho]

Use the NCBI eBot to generate a perl script:

Ebot is an interactive tool that generates a Perl script that implements an E-utility pipeline. Ebot will guide you step by step in building the pipeline and then will download the Perl script to your computer.

To run the script, perl must be installed on your machine along with the following modules available from www.cpan.org:

LWP::Simple
LWP::UserAgent
  

These are very common modules and are part of most standard perl installations.

https://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/ebot/ebot.cgi