def test_sample():
"""
Tests different scenarios of running sample function
"""
import bipype
create_directory('tests/temp')
create_directory('tests/temp/out')
create_directory('tests/temp/other')
create_directory('tests/temp/out/shotgun')
create_directory('tests/temp/out/amplicons')
create_directory('tests/temp/out/amplicons_onlyITS')
create_directory('tests/temp/out/amplicons_only16S')
create_directory('tests/temp/out/biodiversity')
# Scenario 1 - Shotgun
args_1 = preparse_args('@tests/shotgun.opts --out_dir tests/temp/out/shotgun')
opts_1 = bipype.parse_arguments(args_1)
with keeping_directory_clean('tests/data', move_to='tests/temp/other'):
bipype.sample(opts_1)
# Scenario 2 - Amplicons
args_2 = preparse_args('@tests/amplicons.opts --out_dir tests/temp/out/amplicons')
opts_2 = bipype.parse_arguments(args_2)
with keeping_directory_clean('tests/data', move_to='tests/temp/other'):
bipype.sample(opts_2)
#Scenario 3 - Amplicons only ITS
args_3 = preparse_args('@tests/amplicons_onlyITS.opts --out_dir tests/temp/out/amplicons_onlyITS')
opts_3 = bipype.parse_arguments(args_3)
with keeping_directory_clean('tests/data', move_to='tests/temp/other'):
bipype.sample(opts_3)
#Scenario 4 - Amplicons only 16S
args_4 = preparse_args('@tests/amplicons_only16S.opts --out_dir tests/temp/out/amplicons_only16S')
opts_4 = bipype.parse_arguments(args_4)
with keeping_directory_clean('tests/data', move_to='tests/temp/other'):
bipype.sample(opts_4)
#Scenario 5 - Biodiversity
args_5 = preparse_args('@tests/biodiversity.opts --out_dir tests/temp/out/biodiversity')
opts_5 = bipype.parse_arguments(args_5)
with keeping_directory_clean('tests/data', move_to='tests/temp/other'):
bipype.sample(opts_5)
def omit_test_prepare_taxonomy_stats():
"""
Tests different scenarios of running prepare_taxonomy_stats function
"""
import bipype
create_directory('tests/temp')
create_directory('tests/temp/out')
create_directory('tests/temp/other')
create_directory('tests/temp/out/shotgun')
create_directory('tests/temp/out/amplicons')
create_directory('tests/temp/out/amplicons_onlyITS')
create_directory('tests/temp/out/amplicons_only16S')
create_directory('tests/temp/out/biodiversity')
# Scenario 2 - Amplicons
args_2 = preparse_args('@tests/amplicons.opts --out_dir tests/temp/out/amplicons')
opts_2 = bipype.parse_arguments(args_2)
with keeping_directory_clean('tests/data_do_pts/out/amplicons', move_to='tests/temp/other'):
bipype.prepare_taxonomy_stats(opts_2)
#Scenario 3 - Amplicons only ITS
args_3 = preparse_args('@tests/amplicons_onlyITS.opts --out_dir tests/temp/out/amplicons_onlyITS')
opts_3 = bipype.parse_arguments(args_3)
with keeping_directory_clean('tests/data_do_pts/out/amplicons_onlyITS', move_to='tests/temp/other'):
bipype.prepare_taxonomy_stats(opts_3)
#Scenario 4 - Amplicons only 16S
args_4 = preparse_args('@tests/amplicons_only16S.opts --out_dir tests/temp/out/amplicons_only16S')
opts_4 = bipype.parse_arguments(args_4)
with keeping_directory_clean('tests/data_do_pts/out/amplicons_only16S', move_to='tests/temp/other'):
bipype.prepare_taxonomy_stats(opts_4)
#Scenario 5 - Biodiversity
args_5 = preparse_args('@tests/biodiversity.opts --out_dir tests/temp/out/biodiversity')
opts_5 = bipype.parse_arguments(args_5)
with keeping_directory_clean('tests/data_do_pts/out/biodiversity', move_to='tests/temp/other'):
bipype.prepare_taxonomy_stats(opts_5)
# create_directory('tests/temp')
# How to create test?
# 1. create input files for testing exculsively prepare_taxonomy_stats()
# for example: results of shotgun analysis.
# 2. create opts files with proper commands to pass in "opts"
# 3. run test as in the template Scenarios below and
# take a look on output files generated by prepare_taxonomy_stats().
# 4. If an output file looks ok, save it in 'tests' directory,
# adding to filename information allowing to
# recognise later to whith test it belongs.
# For example: if you have output ITS.krona, then save it as my_test_ITS.krona
# 4. replace 'test_1.out' with your filename
# 5. replace 'temp.out' with orginal filename
# 6. repeat steps 4-6 for all output files from prepare_taxonomy_stats()
"""