def main():
tm = bx.phylo.phast.TreeModel.from_file( open( sys.argv[1] ) )
t = bx.phylo.newick.newick_parser.parse_string( tm.tree )
names = sys.argv[2].split( ',' )
nucs = tm.alphabet
background = tm.background
print "#", ','.join( names )
if len( sys.argv ) > 3:
cols = []
for line in open( sys.argv[3] ):
fields = line.rstrip( "\r\n" ).split()
col = fields[0]
# HACK!
col = col.replace( "N", "*" )
cols.append( ( fields[0], int( fields[1]) ) )
a = dict( zip( names, col ) )
lik = felsen( t, a, tm )
# print >>sys.stderr, col
prob = lik_to_prob( lik, background, tm )
print "\t".join( fields + [ ' '.join( map( str, prob ) ) ] )
else:
for rows in cookbook.cross_lists( *( [ nucs ] * len( names ) ) ):
a = dict( zip( names, rows ) )
lik = felsen( t, a, tm )
prob = lik_to_prob( lik, background, tm )
print "\t".join( [ ''.join(rows), "?" , ' '.join( map( str, prob ) ) ] )
counts[col] = 1
# counts = [ ( value, key ) for key, value in counts.iteritems() ]
# counts.sort()
# counts.reverse()
## for count, col in counts:
## print "".join(col), count
options, args = cookbook.doc_optparse.parse(__doc__)
wildcard = False
if options.wildcard:
wildcard = True
max_wildcard = nspecies - 1
if options.maxwildcards:
wildcard = True
max_wildcard = int(options.maxwildcards)
nucs = "ACGT-"
if wildcard:
nucs += "*"
for col in cookbook.cross_lists(*([nucs] * nspecies)):
col = "".join(col)
if wildcard and col.count("*") > max_wildcard:
continue
if col.count("-") == nspecies:
continue
print col, counts.get(col, 0)
