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9ae74ae | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | #!/usr/bin/env python
import distutils.spawn
import os
import sys
sys.path.append(os.path.dirname(distutils.spawn.find_executable("silent_tools.py")))
import silent_tools
from silent_tools import eprint
import re
# Don't throw an error when someone uses head
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE, SIG_DFL)
if (len(sys.argv) == 1):
eprint("")
eprint('silentsequence by bcov - extract the sequences from a silent file')
eprint("Usage:")
eprint(" silentsequence myfile.silent > myfile.seq")
sys.exit(1)
silent_file = sys.argv[1]
silent_index = silent_tools.get_silent_index( silent_file )
with open(silent_file, errors='ignore') as sf:
for tag in silent_index['tags']:
structure = silent_tools.get_silent_structure_file_open( sf, silent_index, tag )
sequence_chunks = silent_tools.get_sequence_chunks( structure )
if (sequence_chunks is None):
continue
sys.stdout.write(" ".join(sequence_chunks) + " " + tag + "\n")
sys.stdout.flush()
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