Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
app
 
 
bin
 
 
 
 
db
 
 
lib
 
 
log
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

##A Web API for GenoCanyon

###Querying Data

As the query can be quite large (~ 1 million coordinates), the API uses POST:

POST /genome

with a JSON data formatted as follows

{
    "chrom": CHROMOSOME_NUMBER,
    "locs":[COORDINATES]
}

Each request requries only one chromosome, and the API returns an array of floating-point values corresponding to the coordinates

####Note:

  1. COORDINATES are assumed to be ordered
  2. The response is ordered in ascending order of the coordinates

####Formatting Data:

format.rb is a formatter for the data, usage:

ruby format.rb FILEPATH CHROM_NUM START_LOC > DEST

It takes a text file with a single floating point value in each line, and labels them with the chromosome number and coordinate specified.

####Database: Please do NOT use the rake commands to create the Database or do migrations. The Database containing the entire scores for hg19 genome has 3095677412 rows and the default structure used by Rails is very slow. The application uses MySQL with the MyISAM engine on the following structure:

Field Type Null Key Default Extra
chrom tinyint(4) NO PRI 0
loc int(11) unsigned NO PRI 0
value decimal(21,20) YES NULL

About

WebAPI for GenoCanyon

Resources

Releases

No releases published

Packages

No packages published