annotate phylogenetic_tree.py @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.

#!/usr/bin/env python

import os
import errno
import sys
import subprocess
import shutil
from Population import Population
import gd_composite

################################################################################

def mkdir_p(path):
  try:
    os.makedirs(path)
  except OSError, e:
    if e.errno <> errno.EEXIST:
      raise

################################################################################

#  <command interpreter="python">
#    phylogenetic_tree.py "$input" "$output" "$output.files_path"
#
#    #if $input_type.choice == '0'
#      "gd_snp"
#      #if $input_type.data_source.choice == '0'
#        "sequence_coverage"
#        "$input_type.data_source.minimum_coverage"
#        "$input_type.data_source.minimum_quality"
#      #else if $input_type.data_source.choice == '1'
#        "estimated_genotype"
#    #else if $input_type.choice == '1'
#      "gd_genotype"
#    #end if
#
#    #if $individuals.choice == '0'
#      "all_individuals"
#    #else if $individuals.choice == '1'
#      "$individuals.p1_input"
#    #end if
#
#    #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
#        "none"
#    #else
#        "$input.metadata.dbkey"
#    #end if
#
#    #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
#    #if $draw_tree_options == ''
#        ""
#    #else
#        "-$draw_tree_options"
#    #end if
#
#    #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
#        #set $arg = '%s:%s' % ($individual_col, $individual_name)
#        "$arg"
#    #end for
#  </command>

################################################################################

# if len(sys.argv) < 11:
#     print >> sys.stderr, "Usage"
#     sys.exit(1)
#
# input, p1_input, output, extra_files_path, minimum_coverage, minimum_quality, dbkey, data_source, draw_tree_options = sys.argv[1:10]
# 
# individual_metadata = sys.argv[10:]
# 
# # note: TEST THIS
# if dbkey in ['', '?', 'None']:
#     dbkey = 'none'
# 
# p_total = Population()
# p_total.from_tag_list(individual_metadata)

if len(sys.argv) < 5:
    print >> sys.stderr, 'Usage'
    sys.exit(1)

input, output, extra_files_path, input_type = sys.argv[1:5]
args = sys.argv[5:]

data_source = '1'
minimum_coverage = '0'
minimum_quality = '0'

if input_type == 'gd_snp':
    data_source_arg = args.pop(0)
    if data_source_arg == 'sequence_coverage':
        data_source = '0'
        minimum_coverage = args.pop(0)
        minimum_quality = args.pop(0)
    elif data_source_arg == 'estimated_genotype':
        pass
    else:
        print >> sys.stderr, 'Unsupported data_source:', data_source_arg
        sys.exit(1)
elif input_type == 'gd_genotype':
    pass
else:
    print >> sys.stderr, 'Unsupported input_type:', input_type
    sys.exit(1)

p1_input, dbkey, draw_tree_options = args[:3]

# note: TEST THIS
if dbkey in ['', '?', 'None']:
    dbkey = 'none'

individual_metadata = args[3:]

p_total = Population()
p_total.from_tag_list(individual_metadata)

################################################################################

mkdir_p(extra_files_path)

################################################################################

def run_program(prog, args, ofh):
    #print "args: ", ' '.join(args)
    p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=ofh, stderr=subprocess.PIPE)
    (stdoutdata, stderrdata) = p.communicate()
    rc = p.returncode
    ofh.close()

    if rc != 0:
        #print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
        print >> sys.stderr, stderrdata
        sys.exit(1)

################################################################################

phylip_outfile = os.path.join(extra_files_path, 'distance_matrix.phylip')
newick_outfile = os.path.join(extra_files_path, 'phylogenetic_tree.newick')
ps_outfile = 'tree.ps'
pdf_outfile = os.path.join(extra_files_path, 'tree.pdf')

################################################################################

informative_snp_file = os.path.join(extra_files_path, 'informative_snps.txt')
mega_distance_matrix_file = os.path.join(extra_files_path, 'mega_distance_matrix.txt')

prog = 'dist_mat'

args = []
args.append(prog)
args.append(input)
args.append(minimum_coverage)
args.append(minimum_quality)
args.append(dbkey)
args.append(data_source)
args.append(informative_snp_file)
args.append(mega_distance_matrix_file)

if p1_input == "all_individuals":
    tags = p_total.tag_list()
else:
    p1 = Population()
    p1.from_population_file(p1_input)
    if not p_total.is_superset(p1):
        print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
        sys.exit(1)
    tags = p1.tag_list()

for tag in tags:
    if input_type == 'gd_genotype':
        column, name = tag.split(':')
        tag = '{0}:{1}'.format(int(column) - 2, name)
    args.append(tag)

fh = open(phylip_outfile, 'w')
run_program(None, args, fh)

################################################################################

prog = 'quicktree'

args = []
args.append(prog)
args.append('-in')
args.append('m')
args.append('-out')
args.append('t')
args.append(phylip_outfile)

fh = open(newick_outfile, 'w')
run_program(None, args, fh)

################################################################################

prog = 'draw_tree'

args = []
args.append(prog)
if draw_tree_options:
    args.append(draw_tree_options)
args.append(newick_outfile)

fh = open(ps_outfile, 'w')
run_program(None, args, fh)

################################################################################

prog = 'ps2pdf'

args = []
args.append(prog)
args.append('-dPDFSETTINGS=/prepress')
args.append(ps_outfile)
args.append('-')

fh = open(pdf_outfile, 'w')
run_program(None, args, fh)

shutil.copyfile(pdf_outfile, output)

################################################################################

info_page = gd_composite.InfoPage()
info_page.set_title('Phylogenetic tree Galaxy Composite Dataset')

display_file = gd_composite.DisplayFile()
display_value = gd_composite.DisplayValue()

out_pdf = gd_composite.Parameter(name='tree.pdf', value='tree.pdf', display_type=display_file)
out_newick = gd_composite.Parameter(value='phylogenetic_tree.newick', name='phylogenetic tree (newick)', display_type=display_file)
out_phylip = gd_composite.Parameter(value='distance_matrix.phylip', name='Phylip distance matrix', display_type=display_file)
out_mega = gd_composite.Parameter(value='mega_distance_matrix.txt', name='Mega distance matrix', display_type=display_file)
out_snps = gd_composite.Parameter(value='informative_snps.txt', name='informative SNPs', display_type=display_file)

info_page.add_output_parameter(out_pdf)
info_page.add_output_parameter(out_newick)
info_page.add_output_parameter(out_phylip)
info_page.add_output_parameter(out_mega)
info_page.add_output_parameter(out_snps)

in_min_cov = gd_composite.Parameter(description='Minimum coverage', value=minimum_coverage, display_type=display_value)
in_min_qual = gd_composite.Parameter(description='Minimum quality', value=minimum_quality, display_type=display_value)

include_ref_value = 'no'
if dbkey != 'none':
    include_ref_value = 'yes'

in_include_ref = gd_composite.Parameter(description='Include reference sequence', value=include_ref_value, display_type=display_value)

if data_source == '0':
    data_source_value = 'sequence coverage'
elif data_source == '1':
    data_source_value = 'estimated genotype'

in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)

branch_type_value = 'square'
if 'd' in draw_tree_options:
    branch_type_value = 'diagonal'

in_branch_type = gd_composite.Parameter(description='Branch type', value=branch_type_value, display_type=display_value)

branch_scale_value = 'yes'
if 's' in draw_tree_options:
    branch_scale_value = 'no'

in_branch_scale = gd_composite.Parameter(description='Draw branches to scale', value=branch_scale_value, display_type=display_value)

branch_length_value = 'yes'
if 'b' in draw_tree_options:
    branch_length_value = 'no'

in_branch_length = gd_composite.Parameter(description='Show branch lengths', value=branch_length_value, display_type=display_value)

tree_layout_value = 'horizontal'
if 'v' in draw_tree_options:
    tree_layout_value = 'vertical'

in_tree_layout = gd_composite.Parameter(description='Tree layout', value=tree_layout_value, display_type=display_value)

info_page.add_input_parameter(in_min_cov)
info_page.add_input_parameter(in_min_qual)
info_page.add_input_parameter(in_include_ref)
info_page.add_input_parameter(in_data_source)
info_page.add_input_parameter(in_branch_type)
info_page.add_input_parameter(in_branch_scale)
info_page.add_input_parameter(in_branch_length)
info_page.add_input_parameter(in_tree_layout)

misc_individuals = gd_composite.Parameter(name='Individuals', value=tags, display_type=gd_composite.DisplayTagList())

info_page.add_misc(misc_individuals)


with open(output, 'w') as ofh:
    print >> ofh, info_page.render()

################################################################################

sys.exit(0)