'''

This script contains examples for reading .gctx files in Python.

'''

import cmap.io.gct as gct

import cmap.io.plategrp as grp

# give input file

path_to_gctx_file = '/xchip/cogs/l1ktools/data/modzs_n272x978.gctx'

# read the full data file

GCTObject = gct.GCT(path_to_gctx_file)

GCTObject.read()

print(GCTObject.matrix)

# read the first 100 rows and 10 columns of the data

GCTObject = gct.GCT(path_to_gctx_file)

GCTObject.read(row_inds=range(100),col_inds=range(10))

print(GCTObject.matrix)

# read the first 10 columns of the data, identified by their

# column ids, stored in a grp file given below

path_to_column_ids = '/xchip/cogs/l1ktools/data/cids_n10.grp'

# read the column ids as a list

column_ids = grp.read_grp(path_to_column_ids)

GCTObject = gct.GCT(path_to_gctx_file)

# extract only the specified columns from the matrix

GCTObject.read(cid=column_ids)

print(GCTObject.matrix)

# get the available meta data headers for data columns and row

column_headers = GCTObject.get_chd()

row_headers = GCTObject.get_rhd()

# get the perturbagen description meta data field from the column data

inames = GCTObject.get_column_meta('pert_iname')

# get the gene symbol meta data field from the row data

symbols = GCTObject.get_row_meta('pr_gene_symbol')

GCTObject.write('/xchip/cogs/l1ktools/data/python_example.gctx')