Esempi in Python per SamtoolsFaidxCommandline.set_parameter

Esempio n. 1

File: test_samtools_tool.py Progetto: sgalpha01/biopython

 def test_faidx(self):
     cmdline = SamtoolsFaidxCommandline(samtools_exe)
     cmdline.set_parameter("reference", self.reference)
     stdout, stderr = cmdline()
     self.assertFalse(
         stderr, f"Samtools faidx failed:\n{cmdline}\nStderr:{stderr}")
     self.assertTrue(os.path.isfile(self.referenceindexfile))

Esempio n. 2

File: test_samtools_tool.py Progetto: MCalvi/biopython

 def test_faidx(self):
     cmdline = SamtoolsFaidxCommandline(samtools_exe)
     cmdline.set_parameter("reference", self.reference)
     stdout, stderr = cmdline()
     self.assertFalse(stderr,
                      "Samtools faidx failed:\n%s\nStderr:%s"
                      % (cmdline, stderr))
     self.assertTrue(os.path.isfile(self.referenceindexfile))

Esempio n. 3

File: test_samtools_tool.py Progetto: kctsai066/hello-world

 def create_fasta_index(self):
     """Create index for reference fasta sequence."""
     cmdline = SamtoolsFaidxCommandline(samtools_exe)
     cmdline.set_parameter("reference", self.reference)
     stdout, stderr = cmdline()

Esempio n. 4

File: test_samtools_tool.py Progetto: kevinwuhoo/biopython

 def create_fasta_index(self):
     """Creates index for reference fasta sequence."""
     cmdline = SamtoolsFaidxCommandline(samtools_exe)
     cmdline.set_parameter("reference", self.reference)
     stdout, stderr = cmdline()