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src/b/i/biopython-HEAD/Tests/test_BWA_tool.py   biopython(Download)
from Bio.Sequencing.Applications import BwaIndexCommandline
from Bio.Sequencing.Applications import BwaAlignCommandline
from Bio.Sequencing.Applications import BwaSamseCommandline
from Bio.Sequencing.Applications import BwaSampeCommandline
 
        def test_samse(self):
            """Test for single end sequencing """
            self.create_fasta_index()
            self.do_aln(self.infile1, self.saifile1)
            cmdline = BwaSamseCommandline(bwa_exe)
            cmdline.set_parameter("reference", self.reference_file)
            cmdline.set_parameter("read_file", self.infile1)
            cmdline.set_parameter("sai_file", self.saifile1)
            stdout, stderr = cmdline(stdout=self.samfile1)

src/b/i/biopython-1.63/Tests/test_BWA_tool.py   biopython(Download)
from Bio import AlignIO
from Bio.Sequencing.Applications import BwaIndexCommandline, BwaAlignCommandline
from Bio.Sequencing.Applications import BwaSamseCommandline, BwaSampeCommandline
from Bio.Sequencing.Applications import BwaBwaswCommandline
from Bio.Application import ApplicationError
    def test_samse(self):
        """Test for single end sequencing """
        cmdline = BwaSamseCommandline()
        cmdline.set_parameter("reference", self.reference_file)
        cmdline.set_parameter("read_file", self.infile1)
        cmdline.set_parameter("sai_file", self.saifile1)
        stdout, stderr = cmdline(stdout=self.samfile1)