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src/b/i/biopython-HEAD/Tests/test_BWA_tool.py   biopython(Download)
import unittest
#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
    def test_index(self):
        """Test for creating index files for the reference genome fasta file"""
        cmdline = BwaIndexCommandline(bwa_exe)
        cmdline.set_parameter("infile", self.reference_file)
        cmdline.set_parameter("algorithm", "bwtsw")
        stdout, stderr = cmdline()
        operation.
        """
        cmdline = BwaIndexCommandline(bwa_exe)
        cmdline.set_parameter("infile", self.reference_file)
        cmdline.set_parameter("algorithm", "bwtsw")
        stdout, stderr = cmdline()

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 test_index(self):
        """Test for creating index files for the reference genome fasta file"""
        cmdline = BwaIndexCommandline()
        cmdline.set_parameter("infile", self.reference_file)
        cmdline.set_parameter("algorithm", "bwtsw")
        stdout, stderr = cmdline()