RF-Cloning.org Forum

gkemp

Member

Registered: 2015-04-13

Posts: 1

Batch script for primer design

Hi everyone! I love this primer design tool and it works great for me. However, I have a list of 50 genes that I want to subclone from another vector, but I have no real scripting skill to make use of this tool using the XML as Steve has suggested. I was wondering if anyone has a script that they are willing to share with me or can direct me to another online tool that will work. It seems that most tools are designed at much more complicated primer design to pull our SNPs or introns from genomic sequences so they don't work for me. Thanks in advance!

Steve Bond

Administrator

Registered: 2014-01-23

Posts: 130

Re: Batch script for primer design

I can probably help you out. Shoot me a private email and we can chat a little bit more about your project details.
-Steve

Steve Bond

Administrator

Registered: 2014-01-23

Posts: 130

Re: Batch script for primer design

If anyone else is interested, I wrote a Python3 script for gkemp that will accept a couple of fasta files (plasmid sequence and insert sequences) along with the insertion sites, and run the batch through the rf-cloning server.
The executable can be found here (Note: if using Chrome, you may need to right-click --> save link as).
From a Unix-like terminal environment, make the program executable:

chmod +x python_soap_client

Then call the program 'help' function to see the list of positional arguments:

./python_soap_client -h

As an example:

./python_soap_client pEGFP-N1.fa inserts.fa "100-200"

You need to have Python3 installed for this to work.
If you're interested in hacking on the script, you can unzip 'python_soap_client' to get at its plain text guts, or just clone the rf-cloning GitHub repo.