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src/b/i/biopython-1.63/Tests/test_BWA_tool.py   biopython(Download)
from Bio import SeqIO
from Bio import AlignIO
from Bio.Sequencing.Applications import BwaIndexCommandline, BwaAlignCommandline
from Bio.Sequencing.Applications import BwaSamseCommandline, BwaSampeCommandline
from Bio.Sequencing.Applications import BwaBwaswCommandline
    def do_aln(self, in_file, out_file):
        """Test for generating sai files given the reference and read file"""
        cmdline = BwaAlignCommandline()
        cmdline.set_parameter("reference", self.reference_file)
        cmdline.read_file = in_file
        self.assertTrue(os.path.isfile(in_file))
        stdout, stderr = cmdline(stdout=out_file)

src/b/i/biopython-HEAD/Tests/test_BWA_tool.py   biopython(Download)
#TODO from Bio.Sequencing.Applications import BwaBwaswCommandline
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 do_aln(self, in_file, out_file):
        """Test for generating sai files given the reference and read file"""
        cmdline = BwaAlignCommandline(bwa_exe)
        cmdline.set_parameter("reference", self.reference_file)
        cmdline.read_file = in_file
        self.assertTrue(os.path.isfile(in_file))
        stdout, stderr = cmdline(stdout=out_file)