Skip to content

Latest commit

 

History

History
117 lines (72 loc) · 2.65 KB

API.md

File metadata and controls

117 lines (72 loc) · 2.65 KB
Raw

Public API

/api/v1/fragments_by_loci/

Type: POST

Body: JSON

The body needs to contain a BEDPE-like array with the loci determening the fragments to be retrieved. Each locus is represented as an array of the following form:

[ chrom1, start1, end1, chrom2, start2, end2, dataUuid, zoomOutLevel ]

The columns need to be of the following form:

  • chrom1 (str):

    First chromosome. E.g., chr1 or 1.

  • start1 (int):

    First start position in base pairs relative to chrom1. E.g., 0 or 1.

  • end1 (int):

    First end position in base pairs relative to chrom1. E.g., chr1 or 1.

  • chrom2 (str):

    Second chromosome. E.g., chr1 or 1.

  • start2 (int):

    Second start position in base pairs relative to chrom2. E.g., 0 or 1.

  • end2 (int):

    Second end position in base pairs relative to chrom2. E.g., chr1 or 1.

  • dataUuid (str):

    UUID of HiGlass server of the tileset representing a Hi-C map. E.g., OHJakQICQD6gTD7skx4EWA.

  • zoomOutLevel (int):

    Inverted zoom level at which the fragment should be cut out. E.g., For GM12878 of Rao et al. (2014) at 1KB resolution, a zoom out level of 0 corresponds to 1KB, 1 corresponds to 2KB, 2 corresponds to 4KB, etc.

For example:

[
  [
    "chr1",
    0,
    500000000,
    "chr1",
    0,
    500000000,
    "uuid-of-my-fancy-hi-c-map",
    0
  ]
]

Parameters:

  • dims (int):

    Width and height of the fragment in pixels. Defaults to 22.

  • padding (int):

    Percental padding related to the dimension of the fragment. E.g., 10 = 10% padding (5% per side). Defaults to 10.

  • percentile (float):

    Percentile clip. E.g., For 99 the maximum will be capped at the 99-percentile. Defaults to 100.0.

  • no-balance (bool):

    If True the fragment will not be balanced using Cooler. Defaults to False.

  • no-normalize (bool):

    If True the fragment will not be normalized to [0, 1]. Defaults to False.

  • ignore-diags (int):

    Number of diagonals to be ignored, i.e., set to 0. Defaults to 0.

  • no-cache (bool):

    If True the fragment will not be retrieved from cache. This is useful for development. Defaults to False.

  • precision (int):

    Determines the float precision of the returned fragment. Defaults to 2.

Return (obj):

{
  "fragments": [
    [
      [0, 0.48, 0, 0.04],
      [0.48, 0, 1, 0.07],
      [0, 1, 0, 0.47],
      [0.04, 0.07, 0.47, 0]
    ],
    ...
  ]
}

(This example comes from a request of /api/v1/fragments_by_loci/?precision=2&dims=4&ignore-diags=1&percentile=99)