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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()