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)
self.assertTrue("fail to locate the index" not in str(stderr) + str(stdout),
"Error aligning sequence to reference:\n%s\nStdout:%s\nStderr:%s\n"
% (cmdline, stdout, stderr))
def PerformBWA(reference_genome,IN_READS): from subprocess import call Refgenome_file=reference_genome print(reference_genome) Input_reads= IN_READS #OUTPUT_file = 'Alignedreads.sam' #f=open(OUTPUT_file,"w") output_sai_file = 'read_1.sai' from Bio.Sequencing.Applications import BwaSamseCommandline from Bio.Sequencing.Applications import BwaAlignCommandline from Bio.Sequencing.Applications import BwaIndexCommandline align_cmd= BwaAlignCommandline(reference=Refgenome_file, read_file=Input_reads) cmd = "bwa index reference_genome"