Command Line tool to generate genotyping primers for Arabidopsis T-DNA lines
This module essentially duplicates the functionality of the SALK Signal T-DNA primer design tool (http://signal.salk.edu/tdnaprimers.2.html) Running setup.py will download the necessary files including the Arabidopsis genome fasta and T-DNA insertion locations from SALK website. After the initial file downloads the tool can be run without an internet connection.
A correspsonding REST API is currently partially implemented, available at https://wh725mphi9.execute-api.us-east-1.amazonaws.com/alpha . See below for endpoints. Full documentation coming soon.
/fasta
/by-gene
/{AGI}
/by-coords
?start=[start coord]&chr=[chromosome number]&bp_upstream=[basepairs upstream to include]&name=[optional name for sequence]&end=[end coords]&orientation=[+ or - strand]&bp_downstream=[basepairs downstream to include]
/by-tdna
/{SALK_ID}
/genes
/get-coords
/{gene}
/tdna
/get-coords
/{SALK_ID}
/get-fasta
/{SALK_ID}