radpipe/stages.py
def process_radtags(self, inputs, output, output_dir, lib, re_1, re_2,
                        extra_options):
        '''Process radtags to separate into separate fastq files'''
        lib_output_dir = os.path.join(output_dir, lib)
        safe_make_dir(lib_output_dir)
        command = "process_radtags -1 {r1} -2 {r2} -b {barcodes_file} " \
                  "-i gzfastq -o {lib_output_dir} --inline_inline --renz_1 {re_1} " \
                  "--renz_2 {re_2} {extra_options} && touch {success_file}".format(
                      r1=inputs[0], r2=inputs[1], barcodes_file=inputs[2],
                      lib_output_dir=lib_output_dir, re_1=re_1, re_2=re_2,
                      extra_options=extra_options, success_file=output)
        run_stage(self.state, "process_radtags", command)
Process radtags to separate into separate fastq files
Process radtags to separate into separate fastq files
Process radtags to separate into separate fastq files
def process_radtags(self, inputs, output, output_dir, lib, re_1, re_2,
                        extra_options):
        lib_output_dir = os.path.join(output_dir, lib)
        safe_make_dir(lib_output_dir)
        command = "process_radtags -1 {r1} -2 {r2} -b {barcodes_file} " \
                  "-i gzfastq -o {lib_output_dir} --inline_inline --renz_1 {re_1} " \
                  "--renz_2 {re_2} {extra_options} && touch {success_file}".format(
                      r1=inputs[0], r2=inputs[1], barcodes_file=inputs[2],
                      lib_output_dir=lib_output_dir, re_1=re_1, re_2=re_2,
                      extra_options=extra_options, success_file=output)
        run_stage(self.state, "process_radtags", command)
def process_radtags ( self , inputs , output , output_dir , lib , re_1 , re_2 , extra_options ) : lib_output_dir = os . path . join ( output_dir , lib ) safe_make_dir ( lib_output_dir ) command = "process_radtags -1 {r1} -2 {r2} -b {barcodes_file} " "-i gzfastq -o {lib_output_dir} --inline_inline --renz_1 {re_1} " "--renz_2 {re_2} {extra_options} && touch {success_file}" . format ( r1 = inputs [ 0 ] , r2 = inputs [ 1 ] , barcodes_file = inputs [ 2 ] , lib_output_dir = lib_output_dir , re_1 = re_1 , re_2 = re_2 , extra_options = extra_options , success_file = output ) run_stage ( self . state , "process_radtags" , command )
Process radtags to separate into separate fastq files
Process radtags to separate into separate fastq files
'''Process radtags to separate into separate fastq files'''
self
inputs
output
output_dir
lib
re_1
re_2
extra_options