model/include/silent_tools/silentremovewatersequence

#!/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) 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

        for idx,i in enumerate( sequence_chunks ):
            i = i.replace( 'w','' )
            i = i.replace( 'v','' )
            sequence_chunks[ idx ] = i

        sys.stdout.write(" ".join(sequence_chunks) + " " + tag + "\n")
        sys.stdout.flush()