bbcflib::gdv Namespace Reference

Functions
def	get_project
def	new_project
def	single_track
def	multiple_tracks
def	send_it
Variables
string	default_url = 'http://gdv.epfl.ch/pygdv'

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Detailed Description

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Module: bbcflib.gdv
===================

Python API for the GDV genome viewer.

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Function Documentation

def bbcflib::gdv::get_project	(		mail,
			key,
			project_key,
			serv_url = default_url
	)

Get a project by it's key.
:param mail : login in TEQUILA
:param key : an user-specific key (ask it to GDV admin)
:param project_key : the project key

def bbcflib::gdv::multiple_tracks	(		mail,
			key,
			serv_url = default_url,
			assembly_id = None,
			project_id = None,
			urls = [],
			fsys_list = [],
			tracknames = [],
			extensions = [],
			force = False
	)

Create tracks on GDV
:param extensions : a list of extensions, separated by whitespace.
:param urls : a list of urls separated by whitespaces. 
:param fsys : if the file is on the same file system, a filesystem path
:param fsys_list :  a list of fsys separated by whitespaces.
:param tracknames : a list of file name, in the same order than the files uploaded.
If there is differents parameters given, the first file uploaded will be file_upload, 
then urls, url, fsys and finally fsys_list. The list is separated by whitespaces.
For other params :see single_track

def bbcflib::gdv::new_project	(		mail,
			key,
			name,
			assembly_id,
			serv_url = default_url
	)

Create a new project on GDV.
:param mail : login in TEQUILA
:param key : an user-specific key (ask it to GDV admin)
:param name : name of the project
:param assembly_id : the assembly identifier in GenRep (must be BBCF_VALID)
:return a JSON

def bbcflib::gdv::send_it	(		url,
			request,
			return_type = 'json'
	)

Send the request to GDV and return the result. As JSON or as a request.read().

def bbcflib::gdv::single_track	(		mail,
			key,
			serv_url = default_url,
			assembly_id = None,
			project_id = None,
			url = None,
			fsys = None,
			trackname = None,
			extension = None,
			force = False,
			delfile = False
	)

Create a new track on GDV.
:param mail : login in TEQUILA
:param key : an user-specific key (ask it to GDV admin)
:param name : name of the project
:param assembly_id : the assembly identifier in GenRep (must be BBCF_VALID). Could be optional if a project_id is specified.
:param project_id : the project identifier to add the track to.
:param url : an url pointing to a file.
:param extension : extension of the file provided.
:param fsys : if the file is on the same file system, a filesystem path
:param trackname : the name to give to the track 
:param force : A boolean. Force the file to be recomputed.
:param delfile : If true and file comming from fsys, the original file will be removed after job success
:return a JSON