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choppy-data-portal-cgdspy

table of contents

Introduction

cgdspy based API for accessing the Cancer Genomics Data Server (CGDS). It's based on cgdsr. Queries the CGDS API and returns available cancer studies. Input is a CGDS object and output is a data.matrix with information regarding the different cancer studies.

Installation

Stable release

To install cgdspy, run this command in your terminal:

pip install cgdspy

This is the preferred method to install cgdspy, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources

The sources for cgdspy can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/go-choppy/cgdspy

Or download the tarball:

$ curl  -OL https://github.com/go-choppy/cgdspy/tarball/master

Once you have a copy of the source, you can install it with:

$ python setup.py install

Usage

To instantiate a new cgds:

import cgdspy
mycgds = cgdspy.CGDSPY("http://www.cbioportal.org/", token = None, verbose = False, ploterrormsg = '')

# get cancer study
mycancerstudy = mycgds.get_cancer_studies()
mycancerstudy = mycancerstudy.iat[1, 0] #'mel_tsam_liang_2017'

# get case list
mycaselist = mycgds.get_case_lists(mycancerstudy)
mycaselist = mycaselist.iat[0, 0] #'mel_tsam_liang_2017_all'

# get genetic profile
mygeneticprofile = mycgds.get_genetic_profiles(mycancerstudy)
mygeneticprofile = mygeneticprofile.iat[0, 0] #'mel_tsam_liang_2017_cna'

# Get data slices for a specified list of genes, genetic profile and case list
gene_list = 'HMGA2'
myprofiledata = mycgds.get_profile_data(gene_list, mygeneticprofile, mycaselist) #data frame

gene_list = ('BRCA1','BRCA2')
myprofiledata = mycgds.get_profile_data(gene_list, mygeneticprofile, mycaselist) #get profile data of two genes

gene_list = 'HMGA2'
mygeneticprofile =  mycgds.get_genetic_profiles(mycancerstudy)
mygeneticprofile = mygeneticprofile.ix[[0, 1], [0]]
# 0           mel_tsam_liang_2017_cna
# 1  mel_tsam_liang_2017_rna_seq_mrna

mygeneticprofile = mygeneticprofile['genetic_profile_id']
myprofiledata = mycgds.get_profile_data(gene_list, mygeneticprofile, mycaselist) # get cna and mrna data

#get clinical data
myclidata = mycgds.get_clinical_data(mycaselist) # get clinical data

Configuration Attributes

backgrounds

Contact

Jun Shang shangjunv@163.com

Your feedbacks are welcome. If you're struggling using the librairy, the best way to ask questions is to use the Github issues so that they are shared with everybody.