def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
temp_file = Wise.align(cmdline, pair, **keywds)
try:
return Statistics(temp_file.name, match, mismatch, gap, extension)
except AttributeError:
try:
keywds['dry_run']
return None
except KeyError:
raise
def align(pair,
scores=None,
gap_start=None,
gap_extension=None,
*args, **keywds):
cmdline = _CMDLINE_PSW[:]
if scores:
cmdline.extend((_OPTION_SCORES, scores))
if gap_start:
cmdline.extend((_OPTION_GAP_START, str(gap_start)))
if gap_extension:
cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
temp_file = Wise.align(cmdline, pair, *args, **keywds)
return parse(temp_file)
def align(pair,
match=_SCORE_MATCH,
mismatch=_SCORE_MISMATCH,
gap=_SCORE_GAP_START,
extension=_SCORE_GAP_EXTENSION,
**keywds):
cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
temp_file = Wise.align(cmdline, pair, **keywds)
try:
return Statistics(temp_file.name, match, mismatch, gap, extension)
except AttributeError:
try:
keywds['dry_run']
return None
except KeyError:
raise