if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("-f", "--fragfiles", nargs="+", required=True, help="")
parser.add_argument("--outfile", required=True, help="")
parser.add_argument("--debug", action="store_true", help="")
opts = parser.parse_args()
# read into fragment as frag[pos] = fragments
offset = 0
out_fraglines = ""
for fragfile in opts.fragfiles:
print fragfile
frag_dict = frag_util.read_fragfile( fragfile )
fraglen = frag_util.get_fraglen( frag_dict )
for pos in frag_dict.keys():
frags = frag_dict[ pos ]
nbrs = sorted( frags.keys() )
for nbr in nbrs:
l = frags[nbr]
if nbr == 0:
assert l.startswith("position:")
n_nbrs = l.split()[3]
out_fraglines += "position:%13s neighbors:%13s\n\n" %( pos+offset, n_nbrs)
continue
out_fraglines += "%s\n\n" % l
offset += (pos+fraglen-1)
#!/usr/bin/env python2.7
from argparse import ArgumentParser
from sys import exit, stderr, stdout
from os import system
from os.path import basename
import frag_util
if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("-f", "--fragfile", required=True, help="")
parser.add_argument("-t", "--top", default=25, type=int, help="")
opts = parser.parse_args()
frag_dict = frag_util.read_fragfile(opts.fragfile)
for pos in frag_dict.keys():
for nbr in range(0, len(frag_dict[pos].keys())):
l = frag_dict[pos][nbr]
if nbr <= opts.top:
if l.startswith("position:"):
print "position:%13s neighbors:%13s\n" % (pos, opts.top)
continue
print l + "\n"