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test_scmatch.py
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test_scmatch.py
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# test results for scmatch...
import os
import subprocess
import shlex
scmatch_path = '/home/yjzhang/Grad_School/bioNLP/scMatch/scMatch.py'
toterms_path = '/home/yjzhang/Grad_School/bioNLP/scMatch/toTerms.py'
ref_path = '/home/yjzhang/Grad_School/bioNLP/scMatch/refDB/FANTOM5'
data_file = 'tm_droplet_data_subset.csv'
run_command = 'python {0} --refType mouse --testType mouse --refDS {1} --dFormat csv --testDS {2}'.format(scmatch_path, ref_path, data_file)
result = subprocess.call(shlex.split(run_command))
run_command = 'python {0} --splF {1} --refDS {2}'.format(toterms_path, 'tm_droplet_data_subset/annotation_result_keep_all_genes', ref_path)
result = subprocess.call(shlex.split(run_command))
data_file = 'tm_droplet_data_means.csv'
run_command = 'python {0} --refType mouse --testType mouse --refDS {1} --dFormat csv --testDS {2}'.format(scmatch_path, ref_path, data_file)
result = subprocess.call(shlex.split(run_command))
run_command = 'python {0} --splF {1} --refDS {2}'.format(toterms_path, 'tm_droplet_data_means/annotation_result_keep_all_genes', ref_path)
result = subprocess.call(shlex.split(run_command))
data_file = 'tm_facs_data_subset.csv'
run_command = 'python {0} --refType mouse --testType mouse --refDS {1} --dFormat csv --testDS {2}'.format(scmatch_path, ref_path, data_file)
result = subprocess.call(shlex.split(run_command))
run_command = 'python {0} --splF {1} --refDS {2}'.format(toterms_path, 'tm_facs_data_subset/annotation_result_keep_all_genes', ref_path)
result = subprocess.call(shlex.split(run_command))
data_file = 'tm_facs_data_means.csv'
run_command = 'python {0} --refType mouse --testType mouse --refDS {1} --dFormat csv --testDS {2}'.format(scmatch_path, ref_path, data_file)
result = subprocess.call(shlex.split(run_command))
run_command = 'python {0} --splF {1} --refDS {2}'.format(toterms_path, 'tm_facs_data_means/annotation_result_keep_all_genes', ref_path)
result = subprocess.call(shlex.split(run_command))