annotate coverage_distributions.py @ 4:7a94f11fe71f

change output.extra_files_path to output.files_path

#!/usr/bin/env python

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

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

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

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

if len(sys.argv) < 7:
    print >> sys.stderr, "Usage"
    sys.exit(1)

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

individual_metadata = []
population_info = []
p1_input = None
all_individuals = False

for arg in sys.argv[5:]:
    if arg == 'all_individuals':
        all_individuals = True
    elif len(arg) > 12 and arg[:12] == 'individuals:':
        p1_input = arg[12:]
    elif len(arg) > 11:
        if arg[:11] == 'population:':
            file, name = arg[11:].split(':', 1)
            population_info.append((file, name))
        elif arg[:11] == 'individual:':
            individual_metadata.append(arg[11:])

p_total = Population()
p_total.from_tag_list(individual_metadata)

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

mkdir_p(extra_files_path)

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

prog = 'coverage'

args = []
args.append(prog)
args.append(input)
args.append(data_source)

user_coverage_file = os.path.join(extra_files_path, 'coverage.txt')
args.append(user_coverage_file)

population_list = []

if all_individuals:
    tags = p_total.tag_list()
elif p1_input is not None:
    p1 = Population()
    this_pop = Population()
    this_pop.from_population_file(p1_input)
    population_list.append(this_pop)
    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()
else:
    tags = []
    for population_file, population_name in population_info:
        population = Population()
        this_pop = Population()
        this_pop.from_population_file(population_file)
        population_list.append(this_pop)
        population.from_population_file(population_file)
        if not p_total.is_superset(population):
            print >> sys.stderr, 'There is an individual in the {} population that is not in the SNP table'.format(population_name)
            sys.exit(1)
        columns = population.column_list()
        for column in columns:
            tags.append('{0}:{1}'.format(column, population_name))

for tag in tags:
    args.append(tag)

## text output
coverage_file = 'coverage.txt'
fh = open(coverage_file, 'w')
#print "args:", ' '.join(args)
p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
rc = p.wait()
fh.close()

## graphical output
fh = open(coverage_file)
coverage2_file = 'coverage2.txt'
ofh = open(coverage2_file, 'w')

for line in fh:
    line = line.rstrip('\r\n')
    elems = line.split('\t')
    name = elems.pop(0)
    values = [ elems[0] ]
    for idx in range(1, len(elems)):
        val = str(float(elems[idx]) - float(elems[idx-1]))
        values.append(val)
    print >> ofh, '{0}\t{1}'.format(name, '\t'.join(values))

fh.close()
ofh.close()

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

prog = 'R'

args = []
args.append(prog)
args.append('--vanilla')
args.append('--quiet')

_realpath = os.path.realpath(__file__)
_script_dir = os.path.dirname(_realpath)
r_script_file = os.path.join(_script_dir, 'coverage_plot.r')

ifh = open(r_script_file)
ofh = open('/dev/null', 'w')
#print "args:", ' '.join(args)
p = subprocess.Popen(args, bufsize=-1, stdin=ifh, stdout=ofh, stderr=None)
rc = p.wait()
ifh.close()
ofh.close()

pdf_file = os.path.join(extra_files_path, 'coverage.pdf')
shutil.copy2('coverage.pdf', pdf_file)
os.remove('coverage.pdf')
os.remove(coverage2_file)

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

info_page = gd_composite.InfoPage()
info_page.set_title('Coverage distributions Galaxy Composite Dataset')

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

out_pdf = gd_composite.Parameter(name='coverage.pdf', value='coverage.pdf', display_type=display_file)
out_txt = gd_composite.Parameter(name='coverage.txt', value='coverage.txt', display_type=display_file)

info_page.add_output_parameter(out_pdf)
info_page.add_output_parameter(out_txt)


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)

info_page.add_input_parameter(in_data_source)

if population_list:
    misc_populations =  gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList())
    info_page.add_misc(misc_populations)
else:
    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)