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Add command option to print align scores #64

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Add command option to print align scores #64

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f3e16ae
Add command option for print align score
h-j-han Jul 19, 2022
8bdef1f
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h-j-han Jul 19, 2022
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17 changes: 14 additions & 3 deletions src/force_align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
# Use the version in realtime for development
class Aligner:

def __init__(self, fwd_params, fwd_err, rev_params, rev_err, heuristic='grow-diag-final-and'):
def __init__(self, fwd_params, fwd_err, rev_params, rev_err, heuristic='grow-diag-final-and', addscore='None'):

build_root = os.path.dirname(os.path.abspath(__file__))
fast_align = os.path.join(build_root, 'fast_align')
Expand All @@ -25,16 +25,23 @@ def __init__(self, fwd_params, fwd_err, rev_params, rev_err, heuristic='grow-dia
self.fwd_align = popen_io(fwd_cmd)
self.rev_align = popen_io(rev_cmd)
self.tools = popen_io(tools_cmd)
self.addscore = addscore

def align(self, line):
self.fwd_align.stdin.write('{}\n'.format(line))
self.rev_align.stdin.write('{}\n'.format(line))
# f words ||| e words ||| links ||| score
fwd_line = self.fwd_align.stdout.readline().split('|||')[2].strip()
rev_line = self.rev_align.stdout.readline().split('|||')[2].strip()
fwd_wholeline = self.fwd_align.stdout.readline()
fwd_line = fwd_wholeline.split('|||')[2].strip()
fwd_score = fwd_wholeline.split('|||')[3].strip()
rev_wholeline = self.rev_align.stdout.readline()
rev_line = rev_wholeline.split('|||')[2].strip()
rev_score = rev_wholeline.split('|||')[3].strip()
self.tools.stdin.write('{}\n'.format(fwd_line))
self.tools.stdin.write('{}\n'.format(rev_line))
al_line = self.tools.stdout.readline().strip()
if self.addscore == 'fwdbwd':
return al_line + '\t' + str(fwd_score) + '\t' + str(rev_score)
return al_line

def close(self):
Expand Down Expand Up @@ -75,6 +82,10 @@ def main():
sys.stderr.write(' {} fwd_params fwd_err rev_params rev_err [heuristic] <in.f-e >out.f-e.gdfa\n'.format(sys.argv[0]))
sys.stderr.write('\n')
sys.stderr.write('where heuristic is one of: (intersect union grow-diag grow-diag-final grow-diag-final-and) default=grow-diag-final-and\n')
sys.stderr.write('To see alignment scores, run:\n')
sys.stderr.write(' {} fwd_params fwd_err rev_params rev_err heuristic fwdbwd <in.f-e >out.f-e.gdfa\n'.format(sys.argv[0]))
sys.stderr.write('\n')
sys.stderr.write('This will show fwd and bwd align score seperated with tab following the alignment pairs.\n')
sys.exit(2)

aligner = Aligner(*sys.argv[1:])
Expand Down