/usr/bin/falcon_ucns_data is in falconkit 0.1.3+20140820-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 | #!/usr/bin/python
#################################################################################$$
# Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted (subject to the limitations in the
# disclaimer below) provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
# GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
# BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
# USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
# SUCH DAMAGE.
#################################################################################$$
import sys
import os
rcmap = dict(zip("ACGTacgtNn-", "TGCAtgcaNn-"))
if __name__ == "__main__":
import argparse
import re
from pbcore.io import FastaReader
tiling_path = {}
with open("all_tiling_path_c") as f:
for l in f:
l = l.strip().split()
tiling_path.setdefault( l[0], [])
offset = int(l[1])
node_id = l[2].split(":")
s = int(l[3])
e = int(l[4])
tiling_path[ l[0] ].append( (offset, node_id[0], node_id[1], s, e) )
f = FastaReader("preads.fa")
seq_db = {}
for r in f:
seq_db[r.name] = r.sequence
f = FastaReader("primary_tigs_c.fa")
p_tigs_db = {}
for r in f:
p_tigs_db[r.name] = r.sequence
for p_tig_id in p_tigs_db:
pread_data = {}
offsets = []
seqs = []
p_tig = p_tigs_db[p_tig_id]
if len(tiling_path[p_tig_id]) <= 5:
continue
print p_tig_id, 0, p_tig
for offset, s_id, end, s, e in tiling_path[p_tig_id]:
seq = seq_db[s_id]
if end == "B":
s, e = e, s
offset = offset - len(seq)
seq = "".join([rcmap[c] for c in seq[::-1]])
else:
offset = offset - len(seq)
print s_id, offset, seq
print "+ + +"
f = FastaReader("a_nodup.fa")
a_tigs_db = {}
for r in f:
a_tigs_db[r.name] = r.sequence
for a_tig_id in a_tigs_db:
pread_data = {}
offsets = []
seqs = []
a_tig = a_tigs_db[a_tig_id]
if len(tiling_path[a_tig_id]) <= 5:
continue
print a_tig_id, 0, a_tig
for offset, s_id, end, s, e in tiling_path[a_tig_id]:
seq = seq_db[s_id]
if end == "B":
s, e = e, s
offset = offset - len(seq)
seq = "".join([rcmap[c] for c in seq[::-1]])
else:
offset = offset - len(seq)
print s_id, offset, seq
print "+ + +"
print "- - -"
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