def test_convert_haps(self):
hapslist = FileConvert.convert_haps(self.good_set)
ref_alt = self.good_set.haps_file.loc[0, 3:4].values.tolist()
hapsalls = hapslist[0][5:]
hapsall_l = []
for a in hapsalls:
if a not in hapsall_l:
hapsall_l.append(a)
self.assertEqual(sorted(ref_alt), sorted(hapsall_l))
def test_start_pedfile(self):
FileParser.check_sample_file(self.good_set)
ped_p = FileConvert.start_pedfile(self.good_set)
self.assertEqual(len(ped_p[0]), 6)
def test_bad_start_pedfile(self):
try:
FileParser.check_sample_file(self.bad_set)
except ValueError:
ped_p = FileConvert.start_pedfile(self.bad_set)
self.assertNotEqual(len(ped_p[0]), 6)
def main():
"""
Argument Parser Function that calls the other components of the code
"""
parser = argparse.ArgumentParser(description = 'Arguments for running the different modules of iLiner',
epilog="For additional help, see xxxx github xxxx")
parser.add_argument('module', choices=['ilash', 'ibd_depth', 'stats'], help='module choice')
parser.add_argument('--sample', '-s', type=str, required=False, help='Sample file with file path')
parser.add_argument('--haps', '-hp', type=str, required=False, help='Phased haplotype file with file path')
parser.add_argument('--genetic_map', '-gm', type=str, required=False, help='Genetic map file with file path')
parser.add_argument('--mapfile', '-mf', type=str, required=False, help='Mapfile made by the ilash module')
parser.add_argument('--outfile_prefix', '-op', type=str, help='Prefix for all of the files produced from this module with file path')
parser.add_argument('--ilash_path', '-i', type=str, required=False, help='File path to ilash')
parser.add_argument('--ilash_output', '-io', type=str, required=False, help='Ilash output, one chromosome for ibd_depth module and all chromosomes for stats module')
parser.add_argument('--population_file', '-pf', type=str, required=False, help='File with individual ids and population [ID]tab[Population]')
parser.add_argument('--vcf', '-v', type=str, required=False, help='Phased VCF with file path')
parser.add_argument('--no_indel', '-ni', action='store_true', required=False, help='Pass if you would like to remove indels from your vcf or haplotype file')
args = parser.parse_args()
log = Logger()
if args.module == 'ilash':
args_dict = vars(args)
log.logger.info('You have selected ilash')
if args_dict['sample'] != None:
log.logger.info("Parsing your sample and haplotype files")
samp_file = LoadFiles.load_sample(args.sample)
if args_dict['haps'] == None:
log.logger.info('Please specify a haplotype file.')
quit()
log.logger.info('Sample file has been loaded')
haps_file = LoadFiles.load_haps(args.haps)
log.logger.info('Haplotype file has been loaded')
ilash_obj = LoadFiles(samp_file, haps_file)
FileParser.check_sample_file(ilash_obj)
log.logger.info('Your sample file has been validated')
FileParser.check_same_sample(ilash_obj)
log.logger.info('Your sample file and haplotype file populations are the same')
if args_dict['no_indel'] == True:
FileParser.remove_indels(ilash_obj)
else:
pass
FileParser.check_alleles(ilash_obj.haps_file.iloc[:,[3]].values, ilash_obj.haps_file.iloc[:,[4]].values)
nucfunc = np.vectorize(FileParser.nucleotide_test)
log_array_ref = nucfunc(ilash_obj.haps_file[[3]])
log_array_alt = nucfunc(ilash_obj.haps_file[[4]])
FileParser.validate_nucleotides(log_array_ref, 'Reference Allele')
FileParser.validate_nucleotides(log_array_alt, 'Alternative Allele')
log.logger.info('Your reference and alternative alleles have been validated')
FileParser.validate_binary(ilash_obj)
log.logger.info('Your haplotypes have been validated')
log.logger.info("Making your map and pedigree files")
pedfile_start = FileConvert.start_pedfile(ilash_obj)
pedlen = int(len(pedfile_start))
hapmap = open(args.genetic_map)
mapfile_str = args.outfile_prefix + ".map"
pedfile_str = args.outfile_prefix + ".ped"
mapfile = open(mapfile_str, 'w')
FileConvert.make_gpos_mapfile(ilash_obj, hapmap, mapfile)
log.logger.info('Your map file has been made')
hapslist = FileConvert.convert_haps(ilash_obj)
final_array = FileConvert.make_pedfile(hapslist, pedlen, pedfile_start)
final_list = final_array.tolist()
pedfile = open(pedfile_str, 'w')
for line in range(len(final_list)):
pedfile.write(' '.join(final_list[line]) + '\n')
pedfile.close()
log.logger.info('Your pedigree file has been made')
log.logger.info('Launching iLASH')
RunIlash.make_param_file(mapfile_str, pedfile_str, args.ilash)
if args_dict['vcf'] != None:
log.logger.info('Your VCF is being parsed')
vcf_file, comments = VcfReader.read_vcf(args.vcf)
vcf_obj = VcfReader(vcf_file, comments)
vcf_header = vcf_file.columns.values.tolist()
VcfParser.validate_header(vcf_header)
VcfParser.validate_chrom(vcf_obj)
if args_dict['no_indel'] == True:
VcfParser.remove_indels(vcf_ojb)
else:
pass
VcfParser.diff_alt_ref(vcf_obj.vcf['REF'], vcf_obj.vcf['ALT'])
log.logger.info('Your VCF has been parsed')
nucfunc = np.vectorize(VcfParser.nucleotide_test)
log_array_ref = nucfunc(vcf_obj.vcf['REF'])
log_array_alt = nucfunc(vcf_obj.vcf['ALT'])
VcfParser.validate_nucleotides(vcf_obj, log_array_ref, 'Reference Allele')
VcfParser.validate_nucleotides(vcf_obj, log_array_alt, 'Alternative Allele')
binary_array = np.isin(vcf_obj.vcf.iloc[:,9:], ['0|0', '0|1', '1|0', '1|1'])
VcfParser.validate_binary(vcf_obj, binary_array)
people = VcfMakeFiles.get_people(vcf_header)
pedfile_start = VcfMakeFiles.start_pedfile(people)
hapslist = VcfMakeFiles.convert_haps(vcf_obj)
#pedlen = int(len(hapslist[0])/2)
pedlen = int(len(haplist[0]/2))
final_array = VcfMakeFiles.make_pedfile(hapslist, pedlen, pedfile_start)
final_list = final_array.tolist()
mapfile_str = args.outfile_prefix + ".map"
pedfile_str = args.outfile_prefix + ".ped"
mapfile = open(mapfile_str, 'w')
pedfile = open(pedfile_str, 'w')
hapmap = open(args.genetic_map)
VcfMakeFiles.make_gpos_mapfile(vcf_obj, hapmap, mapfile)
log.logger.info('Your map file has been made')
for line in range(len(final_list)):
pedfile.write(' '.join(final_list[line]) + '\n')
pedfile.close()
log.logger.info('Your pedigree file has been made')
log.logger.info('Launching iLASH')
RunIlash.make_param_file(mapfile_str, pedfile_str, args.ilash)
if args_dict['sample'] == None and args_dict['vcf'] == None :
log.logger.info('Please specify a sample file or a VCF file.')
elif args.module == 'ibd_depth':
log.logger.info('You have selected ibd_depth')
mapfile = IBDDepth.load_files(args.mapfile)
log.logger.info('Your map file has been loaded')
ilash_output, snps = IBDDepth.load_ilash(args.ilash_output)
log.logger.info('Your ilash output file has been loaded')
mapfile = IBDDepth.find_ibd(mapfile, snps)
four_up, four_down = IBDDepth.get_stdev(mapfile)
IBDDepth.make_depth_plot(mapfile, args.outfile_prefix, four_up, four_down)
log.logger.info('Your IBD depth figures have been made')
log.logger.info('Removing outliers and creating an outlier free file')
IBDDepth.remove_outlier(mapfile, ilash_output, args.outfile_prefix, four_up, four_down)
elif args.module == 'stats':
log.logger.info('You have selected stats')
ilash_results = IBDStats.load_ilash(args.ilash_output)
log.logger.info('Your iLASH output has been loaded')
ilash_pops = IBDStats.load_popfile(args.population_file)
log.logger.info('Your population file has been loaded')
stats_obj = IBDStats(ilash_results, ilash_pops)
IBDStats.remove_self_ibd(stats_obj)
IBDStats.stratify_by_pop(stats_obj)
IBDStats.make_dot_plot(stats_obj, args.outfile_prefix)
log.logger.info('Your pair plot has been made')
IBDStats.make_violin_plot(stats_obj, args.outfile_prefix)
log.logger.info('Your violin plot has been made')
IBDStats.get_ibd_stats(stats_obj, log)
H, pval = (IBDStats.get_kw_h(stats_obj))
log.logger.info('Kruskal-Wallis Test')
log.logger.info('H-statistic: ' + str(H))
log.logger.info('P-Values: ' + str(pval))
if pval < 0.05:
log.logger.info('Reject the null hypothesis - A significant differences exists between groups.')
log.logger.info('Post-hoc Wilcoxon Rank Sum Test')
IBDStats.get_ranksum(stats_obj, log)
else:
log.logger.info('Failure to reject the hypothesis - A significant difference does not exist between the groups')
pop_heatmap = IBDStats.fraction_ibd_sharing(stats_obj)
fig = pop_heatmap.get_figure()
fig.set_size_inches(13.0, 13.0)
fig.savefig(args.outfile_prefix + '_heatmap.png')
log.logger.info('Your heatmap has been made.')