if hasattr(main_tree, "clean_alg_path"):
log.log(28, "Writing root node trimmed alignment @@13:%s@@1:\n %s",
threadname, final_tree_file+".trimmed.fa")
alg = SeqGroup(get_stored_data(main_tree.clean_alg_path))
OUT = open(final_tree_file+".trimmed.fa", "w")
for name, seq, comments in alg:
realname = db.get_seq_name(name)
print >>OUT, ">%s\n%s" %(realname, seq)
OUT.close()
if norender == False:
log.log(28, "Generating tree image for @@13:%s@@1:\n %s",
threadname, final_tree_file+".png")
for lf in main_tree:
lf.add_feature("sequence", alg.get_seq(lf.safename))
try:
from nprlib.visualize import draw_tree
draw_tree(main_tree, GLOBALS[configid], final_tree_file+".png")
except Exception, e:
log.warning('@@8:something went wrong when generating the tree image. Try manually :(@@1:')
if DEBUG:
import traceback, sys
traceback.print_exc(file=sys.stdout)
just_finished_lines.append("Finished %s in %d iteration(s)" %(
threadname, past_threads[configid]))
if GLOBALS["email"]:
if not pending_tasks:
all_lines = finished_lines + just_finished_lines + error_lines
send_mail(GLOBALS["email"], "Your NPR process has ended", '\n'.join(all_lines))
