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src/b/i/biopython-1.63/Tests/test_TCoffee_tool.py   biopython(Download)
import unittest
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import TCoffeeCommandline
 
#Try to avoid problems when the OS is in another language
    def test_TCoffee_1(self):
        """Round-trip through app and read clustal alignment from file
        """
        cmdline = TCoffeeCommandline(t_coffee_exe, infile=self.infile1)
        self.assertEqual(str(cmdline), t_coffee_exe + " -infile Fasta/fa01")
        stdout, stderr = cmdline()
    def test_TCoffee_2(self):
        """Round-trip through app and read pir alignment from file
        """
        cmdline = TCoffeeCommandline(t_coffee_exe, quiet=True)
        cmdline.infile = self.infile1
        cmdline.outfile = self.outfile3
        cmdline.output = "pir_aln"
        self.assertEqual(str(cmdline), t_coffee_exe + " -output pir_aln "
                    "-infile Fasta/fa01 -outfile Fasta/tc_out.pir -quiet")
        stdout, stderr = cmdline()

src/b/i/biopython-HEAD/Tests/test_TCoffee_tool.py   biopython(Download)
import unittest
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import TCoffeeCommandline
 
#Try to avoid problems when the OS is in another language
    def test_TCoffee_1(self):
        """Round-trip through app and read clustal alignment from file
        """
        cmdline = TCoffeeCommandline(t_coffee_exe, infile=self.infile1)
        self.assertEqual(str(cmdline), t_coffee_exe + " -infile Fasta/fa01")
        stdout, stderr = cmdline()
    def test_TCoffee_2(self):
        """Round-trip through app and read pir alignment from file
        """
        cmdline = TCoffeeCommandline(t_coffee_exe, quiet=True)
        cmdline.infile = self.infile1
        cmdline.outfile = self.outfile3
        cmdline.output = "pir_aln"
        self.assertEqual(str(cmdline), t_coffee_exe + " -output pir_aln "
                    "-infile Fasta/fa01 -outfile Fasta/tc_out.pir -quiet")
        stdout, stderr = cmdline()