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Bio.Align.Applications.ProbconsCommandline

All Samples(14)  |  Call(12)  |  Derive(0)  |  Import(2)


src/b/i/biopython-1.63/Tests/test_Probcons_tool.py   biopython(Download)
from Bio._py3k import StringIO
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import ProbconsCommandline
 
#Try to avoid problems when the OS is in another language

    def test_Probcons_alignment_fasta(self):
        """Round-trip through app and read fasta alignment from stdout
        """
        cmdline = ProbconsCommandline(probcons_exe, input=self.infile1)
        self.assertEqual(str(cmdline), probcons_exe + " Fasta/fa01")
        self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
        stdout, stderr = cmdline()

    def test_Probcons_alignment_clustalw(self):
        """Round-trip through app and read clustalw alignment from stdout
        """
        cmdline = ProbconsCommandline(probcons_exe)
        cmdline.set_parameter("input", "Fasta/fa01")
        cmdline.clustalw = True
        self.assertEqual(str(cmdline), probcons_exe + " -clustalw Fasta/fa01")
        self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
        stdout, stderr = cmdline()


src/b/i/biopython-HEAD/Tests/test_Probcons_tool.py   biopython(Download)
from Bio._py3k import StringIO
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import ProbconsCommandline
 
#Try to avoid problems when the OS is in another language

    def test_Probcons_alignment_fasta(self):
        """Round-trip through app and read fasta alignment from stdout
        """
        cmdline = ProbconsCommandline(probcons_exe, input=self.infile1)
        self.assertEqual(str(cmdline), probcons_exe + " Fasta/fa01")
        self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
        stdout, stderr = cmdline()

    def test_Probcons_alignment_clustalw(self):
        """Round-trip through app and read clustalw alignment from stdout
        """
        cmdline = ProbconsCommandline(probcons_exe)
        cmdline.set_parameter("input", "Fasta/fa01")
        cmdline.clustalw = True
        self.assertEqual(str(cmdline), probcons_exe + " -clustalw Fasta/fa01")
        self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
        stdout, stderr = cmdline()