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

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.

mrna batch
• 2,786 views • link
updated by Carambakaracho Carambakaracho • written by Shicheng Guo Shicheng Guo
  • You can use NCBI unix utils and a loop to go through your gene ID's.
  • You can use Ensembl REST (or Perl) API
• 1 views • link
written by GenoMax GenoMax

1 answer

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

• 1 views • link
written by Carambakaracho Carambakaracho

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