Project for prototyping ideas for "D4 server". Initially bigwig is used as a proxy for d4 files.
You need a recent version of python, tested with 3.9, and pip
pip install -r requirements.txt
python d4_server.py
The server will now be listening on port 8888. You can change the port by editing d4_server.py
The basic URL syntax to use with IGV is as follows
- scheme: htsget
- path: full path to a bigwig file on the machine running the server. Spaces should be percent encoded (
%20)
Example
d4get://localhost:8888/Users/jrobinso/igv-team%20Dropbox/Data/Juicebox/CTCF_Untreated.bw
IGV assumes the transport protocol for the d4get scheme is http. This is analogous to how the htsget scheme is handled.
If we retain the scheme-based syntax we might add d4gets to signal https protocol (with htsget we just assume https).
The following isn't required for igv use, but might be useful for testing. The server uses the GET method with parameters. Parameters can be
- none, in which case nothing is returned
- class=header, which currently returns the chromosome names as a json array. This is important for IGV to be able do chr name aliasing.
- chr=str&start=int&end=int, data query, returns a binary response as described below.
Data query response is simply a binary stream of bytes in the following order. In a real implementation we would gzip this.
- start (uint) - the genomic start position of the data, should be same as the query parameter
- step (uint) - genomic step (bin) size for each data point
- npoints (uint) - the number of data points
- data (float) - array of float data