Expand description
Parser implementation for matrices in JASPAR (2016) format.
The JASPAR database stores manually curated DNA-binding sites as count matrices.
The JASPAR files contains a FASTA-like header line for each record, followed by one line per symbol storing tab-separated counts at each position. The 2016 version introduces bracketed matrix columns for each symbol, allowing for non-standard alphabets to be used:
>MA0001.3 AGL3
A [ 0 0 82 40 56 35 65 25 64 0 ]
C [ 92 79 1 4 0 0 1 4 0 0 ]
G [ 0 0 2 3 1 0 4 3 28 92 ]
T [ 3 16 10 48 38 60 25 63 3 3 ]Structs§
Functions§
- read
- Read the records from a file in JASPAR (2016) format.