radpipe/stages.py
def bowtie_index(self, input, outputs, reference_dir):
        '''Index reference genome for bowtie alignment'''
        safe_make_dir(reference_dir)
        command = "ln -sf {ref_fasta} {ref_symlink} && bowtie-build " \
                  "{ref_symlink} {index_base}".format(
                      ref_fasta=os.path.abspath(input),
                      ref_symlink=os.path.join(reference_dir, "reference.fa"),
                      index_base= os.path.join(reference_dir, "reference"))
        run_stage(self.state, "build_index", command)
Index reference genome for bowtie alignment
Index reference genome for bowtie alignment
Index reference genome for bowtie alignment
def bowtie_index(self, input, outputs, reference_dir):
        safe_make_dir(reference_dir)
        command = "ln -sf {ref_fasta} {ref_symlink} && bowtie-build " \
                  "{ref_symlink} {index_base}".format(
                      ref_fasta=os.path.abspath(input),
                      ref_symlink=os.path.join(reference_dir, "reference.fa"),
                      index_base= os.path.join(reference_dir, "reference"))
        run_stage(self.state, "build_index", command)
def bowtie_index ( self , input , outputs , reference_dir ) : safe_make_dir ( reference_dir ) command = "ln -sf {ref_fasta} {ref_symlink} && bowtie-build " "{ref_symlink} {index_base}" . format ( ref_fasta = os . path . abspath ( input ) , ref_symlink = os . path . join ( reference_dir , "reference.fa" ) , index_base = os . path . join ( reference_dir , "reference" ) ) run_stage ( self . state , "build_index" , command )
Index reference genome for bowtie alignment
Index reference genome for bowtie alignment
'''Index reference genome for bowtie alignment'''
self
input
outputs
reference_dir