Takes a MrBayes .t file and writes (to standard out) a .p file with the parameters being the edge lengths for each of the Terminal edges.

terminal_edges_to_dot_p.py

#!/usr/bin/env python
'''Takes a MrBayes .t file and writes (to standard out) a .p file with
the parameters being the edge lengths for each of the Terminal edges.

This .p file can be used with Tracer http://tree.bio.ed.ac.uk/software/tracer/
or other MCMC diagnostics files.

Example invocation with redirection to a file called term_edges_myrun.p :

    python terminal_edges_to_dot_p.py myrun.t > term_edges_myrun.p

'''

import sys
import re
try:
    fn = sys.argv[1]
except:
    inp = sys.stdin
else:
    try:
        inp = open(fn, 'rU')
    except:
        sys.exit('Error opening ' + fn + '\n')
inp_iter = iter(inp)

try:
    trans_pat = re.compile('^\s+(\d+)\s.*([,;])\s*\n')
    m = None
    while not m:
        line = inp_iter.next()
        m = trans_pat.match(line)
    for line in inp_iter:
        prev_m = m
        m = trans_pat.match(line)
        if not m:
            break
    ntax = int(prev_m.group(1))
except:
    sys.exit('Error in detecting the number of taxa\n')
sys.stderr.write(str(ntax) + ' leaves detected\n')

tree_pat = re.compile('^\s*tree rep\.(\d+)')
rep_str_list = []
edge_len_lists = [[] for i in range(ntax)]
edge_len_pats = [re.compile('[(,]' + str(i + 1) + ':([-0-9.eE]+)[),]') for i in range(ntax)]

outp = sys.stdout
outp.write('Gen')
for i in range(ntax):
    outp.write('\tedge' + str(i + 1))
outp.write('\n')
try:
    while True:
        m = tree_pat.match(line)
        if m:
            rep_str = m.group(1)
            # rep_str_list.append(rep_str)
            outp.write(rep_str + '\t')
            row_str = []
            for i, pat in enumerate(edge_len_pats):
                m2 = pat.search(line)
                if not m2:
                    sys.exit('Edge pattern not found for leaf ' + str(i+1) + ' in rep.' + rep_str)
                f_str = m2.group(1)
                e = float(f_str)
                # edge_len_lists[i].append(e)
                row_str.append(f_str)
            outp.write('\t'.join(row_str))
            outp.write('\n')
        else:
            rsl = line.rstrip()
            if rsl:
                sys.stderr.write('Skipping line "' + rsl[:10] + '"...\n')
        line = inp_iter.next()
except StopIteration:        
    sys.exit(0)