#Dan Blankenberg

#takes fasta alignments, a distance metric and builds neighbor joining trees

import os, sys

from galaxy import eggs

from galaxy.tools.util import hyphy_util



#Retrieve hyphy path, this will need to be the same across the cluster

tool_data = sys.argv.pop()

HYPHY_PATH = os.path.join( tool_data, "HYPHY" )

HYPHY_EXECUTABLE = os.path.join( HYPHY_PATH, "HYPHY" )



#Read command line arguments

input_filename = os.path.abspath(sys.argv[1].strip())

output_filename1 = os.path.abspath(sys.argv[2].strip())

output_filename2 = os.path.abspath(sys.argv[3].strip())

distance_metric = sys.argv[4].strip()

temp_ps_filename = hyphy_util.get_filled_temp_filename("")



#Guess if this is a single or multiple FASTA input file

found_blank = False

is_multiple = False

for line in open(input_filename):

    line = line.strip()

    if line == "": found_blank = True

    elif line.startswith(">") and found_blank:

        is_multiple = True

        break

    else: found_blank = False



NJ_tree_shared_ibf = hyphy_util.get_filled_temp_filename(hyphy_util.NJ_tree_shared_ibf)



#set up NJ_tree file

NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_tree(NJ_tree_shared_ibf))

#setup Config file

config_filename = hyphy_util.get_nj_tree_config_filename(input_filename, distance_metric, output_filename1, temp_ps_filename, NJ_tree_filename)

if is_multiple: 

    os.unlink(NJ_tree_filename)

    os.unlink(config_filename)

    NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_treeMF(NJ_tree_shared_ibf))

    config_filename = hyphy_util.get_nj_treeMF_config_filename(input_filename, output_filename1, temp_ps_filename, distance_metric, NJ_tree_filename)

    print "Multiple Alignment Analyses"

else: print "Single Alignment Analyses"





#Run Hyphy

hyphy_cmd = "%s BASEPATH=%s USEPATH=/dev/null %s" % (HYPHY_EXECUTABLE, HYPHY_PATH, config_filename)

hyphy = os.popen(hyphy_cmd, 'r')

#print hyphy.read()

hyphy.close()



#remove temporary files

os.unlink(NJ_tree_filename)

os.unlink(config_filename)





#Convert PS to PDF

if os.path.getsize(temp_ps_filename)>0: temp = os.popen("ps2pdf %s %s" % (temp_ps_filename, output_filename2), 'r').close()

os.unlink(temp_ps_filename)