WARNING | OUTDATED:

This repo is not actively maintained any more. Please use HiGlass Server instead. The code and functionality as be merged and is continuously expanded.

HiPiler Server

This is a clean clone of HiGlass Server extended with extra endpoints for HiPiler

Installation

git clone https://github.com/hms-dbmi/higlass-server mdm-server && cd mdm-server
mkvirtualenv -a $(pwd) mdm-server
pip install cython
pip install --upgrade -r requirements.txt
./manage.py migrate
./manage.py runserver localhost:8000

Content

Add Data

These steps are optional in case one wants to start with a pre-populated database.

COOL=dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool
HITILE=wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile

wget https://s3.amazonaws.com/pkerp/public/$COOL
mv $COOL data/

wget https://s3.amazonaws.com/pkerp/public/$HITILE
mv $HITILE data/

curl -F "datafile=@data/$COOL" -F "filetype=cooler" -F "datatype=matrix" -F "uid=aa" http://localhost:8000/tilesets/
curl -F "datafile=@data/$HITILE" -F "filetype=hitile" -F "datatype=vector" -F "uid=bb" http://localhost:8000/tilesets/

The "uid" parameter is optional, and if it were missing, one would be generated. This uuid can be used to retrieve tiles:

Get tileset info:

curl http://localhost:8000/tileset_info/?d=aa

Get a tile:

curl http://localhost:8000/tiles/?d=aa.0.0.0

Preparing Cooler Files

Cooler files store Hi-C data. They need to be decorated with aggregated data at multiple resolutions in order to work with higlass-server. This is easily accomplished by simply installing the cooler python package and running the recursive_agg_onefile.py script. For now this has to come from a clone of the official cooler repository, but this will hopefully be merged into the main branch shortly.


git clone -b develop https://github.com/pkerpedjiev/cooler.git
cd cooler
python setup.py install

recursive_agg_onefile.py file.cooler --out output.cooler

Preparing bigWig files for use with `higlass-server`

BigWig files contain values for positions along a genome. To be viewable using higlass, they need to be aggregated using clodius:

Installing clodius:

pip install clodius

Getting a sample dataset:

wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig

Aggregate it:

tile_bigWig.py wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig --output-file data/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile

curl -H "Content-Type: application/json" -X POST -d '{"processed_file":"data/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2","file_type":"hitile"}' http://localhost:8000/tilesets/

Unit tests

wget -O -P data/ https://s3.amazonaws.com/pkerp/public/dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool
wget -O -P data/ https://s3.amazonaws.com/pkerp/public/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile
wget -O -P data/ https://s3.amazonaws.com/pkerp/public/gene_annotations.short.db

python manage.py test tilesets

Upgrade

bumpversion patch

Examples

Queries

GET: /api/v1/fragments_by_chr/?precision=2&cooler=Rao2014-GM12878-MboI-allreps-filtered.1kb.multires.cool&zoomout-level=2&chrom=22&loop-list=GSE63525_GM12878_primary%2breplicate_HiCCUPS_looplist.txt

Note: cooler can also be the uuid specified for higlass, e.g., rao1kbmr

Response:

{
  "count": 163,
  "dims": 22,
  "fragments": [
    {
      "end1": 17400000,
      "end2": 17540000,
      "matrix": [
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0.3,0,0,0,0,0,0.33,0.49,0.4,0.6,0.63,0.79,0.57,0.4,0.5,0.26,0.27,0.18,0.11,0.17,0.22,0.25],
        [0.44,0,0,0,0,0,0.6,0.42,0.56,0.6,0.84,1,0.69,0.69,0.4,0.31,0.31,0.31,0.3,0.17,0.13,0.13],
        [0.34,0,0,0,0,0,0.18,0.46,0.56,0.67,0.62,0.84,0.64,0.8,0.3,0.41,0.31,0.43,0.3,0.15,0.15,0.24],
        [0.47,0,0,0,0,0,0.69,0.49,0.45,0.66,0.71,0.69,0.77,0.5,0.44,0.37,0.21,0.14,0.22,0.19,0.23,0.14],
        [0.49,0,0,0,0,0,0.39,0.48,0.42,0.52,0.45,0.67,0.59,0.47,0.42,0.29,0.24,0.3,0.16,0.14,0.17,0.11],
        [0.47,0,0,0,0,0,0.32,0.32,0.51,0.41,0.55,0.6,0.52,0.46,0.44,0.29,0.3,0.18,0.27,0.28,0.16,0.14],
        [0.24,0,0,0,0,0,0.68,0.18,0.36,0.52,0.41,0.59,0.35,0.32,0.42,0.33,0.19,0.19,0.21,0.25,0.1,0.29],
        [0.67,0,0,0,0,0,0.56,0.4,0.57,0.33,0.44,0.66,0.2,0.31,0.38,0.29,0.23,0.16,0.38,0.21,0.28,0.25],
        [0.59,0,0,0,0,0,0.2,0.39,0.43,0.49,0.43,0.66,0.42,0.34,0.31,0.25,0.29,0.16,0.2,0.14,0.11,0.27],
        [0.44,0,0,0,0,0,0.31,0.45,0.45,0.47,0.45,0.38,0.57,0.29,0.32,0.18,0.29,0.28,0.25,0.26,0.17,0.12],
        [0.43,0,0,0,0,0,0.45,0.21,0.37,0.57,0.25,0.53,0.34,0.43,0.25,0.32,0.17,0.22,0.28,0.21,0.18,0.15],
        [0.58,0,0,0,0,0,0.54,0.36,0.36,0.36,0.4,0.4,0.26,0.28,0.28,0.23,0.26,0.23,0.29,0.2,0.12,0.16]
      ],
      "start2": 17535000,
      "start1": 17395000,
      "chrom1": "22",
      "chrom2": "22"
    },
    ...
  ],
  "relativeLoci": true,
  "zoomoutLevel": 2
}

POST: /api/v1/fragments_by_loci/

Note: cooler can also be the uuid specified for higlass, e.g., rao1kbmr

Data:

{
  "cooler": "Rao2014-GM12878-MboI-allreps-filtered.1kb.multires.cool",
  "precision": 2,
  "zoomoutLevel": 2,
  "loci": [
    {
      "end1": 17400000,
      "end2": 17540000,
      "start2": 17535000,
      "start1": 17395000,
      "chrom1": "22",
      "chrom2": "22"
    }
  ]
}

Response:

{
  "count": 1,
  "dim": 22,
  "fragments": [
    {
      "end1": 17400000,
      "end2": 17540000,
      "matrix": [
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
        [0.3,0,0,0,0,0,0.33,0.49,0.4,0.6,0.63,0.79,0.57,0.4,0.5,0.26,0.27,0.18,0.11,0.17,0.22,0.25],
        [0.44,0,0,0,0,0,0.6,0.42,0.56,0.6,0.84,1,0.69,0.69,0.4,0.31,0.31,0.31,0.3,0.17,0.13,0.13],
        [0.34,0,0,0,0,0,0.18,0.46,0.56,0.67,0.62,0.84,0.64,0.8,0.3,0.41,0.31,0.43,0.3,0.15,0.15,0.24],
        [0.47,0,0,0,0,0,0.69,0.49,0.45,0.66,0.71,0.69,0.77,0.5,0.44,0.37,0.21,0.14,0.22,0.19,0.23,0.14],
        [0.49,0,0,0,0,0,0.39,0.48,0.42,0.52,0.45,0.67,0.59,0.47,0.42,0.29,0.24,0.3,0.16,0.14,0.17,0.11],
        [0.47,0,0,0,0,0,0.32,0.32,0.51,0.41,0.55,0.6,0.52,0.46,0.44,0.29,0.3,0.18,0.27,0.28,0.16,0.14],
        [0.24,0,0,0,0,0,0.68,0.18,0.36,0.52,0.41,0.59,0.35,0.32,0.42,0.33,0.19,0.19,0.21,0.25,0.1,0.29],
        [0.67,0,0,0,0,0,0.56,0.4,0.57,0.33,0.44,0.66,0.2,0.31,0.38,0.29,0.23,0.16,0.38,0.21,0.28,0.25],
        [0.59,0,0,0,0,0,0.2,0.39,0.43,0.49,0.43,0.66,0.42,0.34,0.31,0.25,0.29,0.16,0.2,0.14,0.11,0.27],
        [0.44,0,0,0,0,0,0.31,0.45,0.45,0.47,0.45,0.38,0.57,0.29,0.32,0.18,0.29,0.28,0.25,0.26,0.17,0.12],
        [0.43,0,0,0,0,0,0.45,0.21,0.37,0.57,0.25,0.53,0.34,0.43,0.25,0.32,0.17,0.22,0.28,0.21,0.18,0.15],
        [0.58,0,0,0,0,0,0.54,0.36,0.36,0.36,0.4,0.4,0.26,0.28,0.28,0.23,0.26,0.23,0.29,0.2,0.12,0.16]
      ],
      "start2": 17535000,
      "start1": 17395000,
      "chrom1": "22",
      "chrom2": "22"
    }
  ],
  "relativeLoci": true,
  "zoomoutLevel": 2
}

GET: /api/v1/loci?chrom=22&loop-list=GSE63525_GM12878_primary%2breplicate_HiCCUPS_looplist.txt

Response:

{
  "loci": [
    {
      "end1": 17400000,
      "end2": 17540000,
      "start2": 17535000,
      "start1": 17395000,
      "chrom1": "22",
      "chrom2": "22"
    },
    ...

flekschas / hipiler-server Goto Github PK

hipiler-server's Introduction

HiPiler Server

Installation

Content

Add Data

Preparing Cooler Files

Preparing bigWig files for use with `higlass-server`

Unit tests

Upgrade

Examples

Queries

hipiler-server's People

Contributors

Stargazers

Watchers

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent

flekschas / hipiler-server Goto Github PK

hipiler-server's Introduction

HiPiler Server

Installation

Content

Add Data

Preparing Cooler Files

Preparing bigWig files for use with higlass-server

Unit tests

Upgrade

Examples

Queries

hipiler-server's People

Contributors

Stargazers

Watchers

Recommend Projects

Recommend Topics

Recommend Org

Preparing bigWig files for use with `higlass-server`