jvrana
commented
7 years ago Hi Bjorn,
Thanks for reaching out. I apologize for the thin documentation. I will be updating the documentation soon with some better examples, as well as adding new alignments and proteins features to this API-wrapper.
This repo is just a python wrapper for Benchling's API with some extra convenience methods. Our lab collaborates with many other labs and groups and shares DNA mainly through Benchling, usually via the Benchling share links. Additionally, we use suite of different programs for designing DNAs (e.g. Coral or your own pydna package). This repo serves as a link between these software packages and the DNA data we store on Benchling. There are also some features provided by this repo that currently do not exist in Benchling that are very useful, mainly the 'search' function which allows you to search your entire Benchling database for a particular sequence or use regular expressions to find folders+sequences.
I use this repo for:
- Searching Benchling databases using regular expressions (e.g. find anything with "Cas9" or "crispr" in the name)
- Searching entire Benchling database + collaborators databases for a particular DNA sequence or name
- Converting Benchling share link to gb or fasta format (as in a Jupyter Notebook)
- Quickly changing the names of hundreds of Benchling plasmids
- Quickly adding tags to hundreds of Benchling plasmids\
- Programmatically create new sequences that automatically upload to Benching (e.g. DNA libraries)
- Automatically submitting Benchling sequence alignments from Sanger sequencing data (e.g. scripts automatically fire a Benchling alignment when a folder sees a new .ab1 file)
dgretton
Hi, this looks very interesting. What is your use case?