#Dan Blankenberg

#takes commandline tree def and input multiple fasta alignment file and runs the branch length ananlysis

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

tree_contents = sys.argv[3].strip()

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

base_freq = sys.argv[5].strip()

model_options = sys.argv[6].strip()



#Set up Temporary files for hyphy run

#set up tree file

tree_filename = hyphy_util.get_filled_temp_filename(tree_contents)



#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



#set up BranchLengths file

BranchLengths_filename = hyphy_util.get_filled_temp_filename(hyphy_util.BranchLengths)

if is_multiple: 

    os.unlink(BranchLengths_filename)

    BranchLengths_filename = hyphy_util.get_filled_temp_filename(hyphy_util.BranchLengthsMF)

    print "Multiple Alignment Analyses"

else: print "Single Alignment Analyses"



#setup Config file

config_filename = hyphy_util.get_branch_lengths_config_filename(input_filename, nuc_model, model_options, base_freq, tree_filename, output_filename, BranchLengths_filename)



#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(BranchLengths_filename)

os.unlink(tree_filename)

os.unlink(config_filename)