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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Tests the basic functionality of the GEO parsers.
"""
from __future__ import print_function
import os
import sys
import Bio.Geo
testfiles = ['GSE16.txt', 'GSM645.txt', 'GSM691.txt', 'GSM700.txt', 'GSM804.txt']
# Five additional files from the NCBI to document the GEO SOFT file format
# changes made in 2005. Note the new table_begin and table_end lines.
testfiles.extend(['soft_ex_affy.txt',
'soft_ex_affy_chp.txt',
'soft_ex_dual.txt',
'soft_ex_family.txt',
'soft_ex_platform.txt',
'soft_ex_series.txt'])
for file in testfiles:
if sys.version_info[0] >= 3:
# Python 3 problem: Can't use utf8 on Tests/Geo/soft_ex_*.txt
# due to micro (\xb5) and degrees (\xb0) symbols
fh = open(os.path.join("Geo", file), encoding="latin")
else:
fh = open(os.path.join("Geo", file))
print("Testing Bio.Geo on " + file + "\n\n")
records = Bio.Geo.parse(fh)
for record in records:
print(record)
print("\n")
fh.close()
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