def create_gmap_reference(reference_dir, reference_path, reference_name,
parameters=None):
'It creates the reference fpath'
cmd = ['gmap_build', '-B', get_external_bin_dir(), '-D', reference_dir,
'-d', reference_name]
if parameters and 'kmer' in parameters:
cmd.extend(['-k', str(parameters['kmer'])])
cmd.append(reference_path)
call(cmd,raise_on_error=True)
fpath = '%s.coords' % reference_name
if os.path.exists(fpath):
os.remove(fpath)
def _modify_gmap_makefile(makefile):
'It modifies the gmap makefile to use proper binaries'
fhand = NamedTemporaryFile(delete=False)
bin_dir = get_external_bin_dir()
for line in open(makefile):
if line.startswith('FA_COORDS'):
line = 'FA_COORDS = %s/fa_coords\n' % bin_dir
if line.startswith('MD_COORDS'):
line = 'MD_COORDS = %s/md_coords\n' % bin_dir
if line.startswith('GMAP_PROCESS'):
line = 'GMAP_PROCESS = %s/gmap_process\n' % bin_dir
if line.startswith('GMAPINDEX'):
line = 'GMAPINDEX = %s/gmapindex\n' % bin_dir
if line.startswith('PMAPINDEX'):
line = 'PMAPINDEX = %s/pmapindex\n' % bin_dir
fhand.write(line)
fhand.flush()
shutil.move(fhand.name, makefile)
