def test_normal_fa_run(self): """ Tests taggd demultiplexer on a variety of small files. """ outdir = tempfile.mkdtemp(prefix="taggd_demultiplex_test_out_fasta_") args = ["--k", "4", "--max-edit-distance", "8", "--overhang", "3", "--subprocesses", "3", "--seed", "dsfiogwhgfsaeadsgfADSgsagaagd"] args += [self.inbarcodes, self.infa, os.path.join(outdir, "outfile")] # Start the demultiplexer try: print "\n# Running Fasta test with parameters: " + " ".join(args) deplex.main(args) self.validate_output_data("Normal Fasta test", "fa", outdir) except Exception as e: print e self.assertTrue(0, "Running Normal Fasta test failed\n")
def test_normal_fa_run(self): """ Tests taggd demultiplexer on a variety of small files. """ outdir = tempfile.mkdtemp(prefix="taggd_demultiplex_test_out_fasta_") args = ["--k", "4", "--max-edit-distance", "8", "--overhang", "3", "--subprocesses", "3", "--seed", "dsfiogwhgfsaeadsgfADSgsagaagd"] args += [self.inbarcodes, self.infa, os.path.join(outdir, "outfile")] # Start the demultiplexer try: print("\n# Running Fasta test with parameters: " + " ".join(args)) deplex.main(args) self.validate_output_data("Normal Fasta test", "fa", outdir) except Exception as e: print(e) self.assertTrue(0, "Running Normal Fasta test failed\n")
#!/usr/bin/env python """ Starts and runs a TagGD demultiplexing job. Type -h for help. \n See https://github.com/JoelSjostrand/taggd/wiki for manual and the most recent source code. \n See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057521 for the peer-reviewed reference to the program. """ import taggd.core.demultiplex as deplex if __name__ == "__main__": deplex.main()
#!/usr/bin/env python """ Starts and runs a TagGD demultiplexing job. Type -h for help. \n See https://github.com/SpatialTranscriptomicsResearch/taggd/wiki for manual and the most recent source code. \n See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057521 for the peer-reviewed reference to the program. """ import taggd.core.demultiplex as deplex if __name__ == "__main__": deplex.main()