silentsequence

#!/usr/bin/env python

import os
import sys
# if you pip installed this is wrong but you have silent_tools installed anyways
silent_tools_dir = os.path.dirname(os.path.realpath(__file__))
if silent_tools_dir not in sys.path:
    sys.path.append(silent_tools_dir)

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()