def calc_enrichment(args):
genotype_folder = args['genotype_folder']
genes_files = args['genes_file']
gwas_file = args['gwas_file']
log.info('Retrieving genes')
genes = {}
for genes_file in genes_files:
with open(genes_file, 'r') as f:
genes[os.path.basename(genes_file)] = json.load(f)
gwas_result = None
_, input_ext = os.path.splitext(gwas_file)
log.info('Opening GWAS file')
if input_ext == '.csv':
gwas_result = result.load_from_csv(gwas_file)
else:
gwas_result = result.load_from_hdf5(gwas_file)
log.info('Loading genotype file')
genotype_data = _load_genotype_(genotype_folder)
top_snps = gwas_result.get_top_snps(args['top_snps_count'])
top_snps.sort(order=['scores'])
top_snps = top_snps[:args['top_snps_count']]
pval = enrichment.enrichment(genes, genotype_data, top_snps,
args['window_size'],
args['permutation_count'])
print json.dumps(pval)
return pval
def calc_enrichment(args):
genotype_folder = args['genotype_folder']
genes_files = args['genes_file']
gwas_file = args['gwas_file']
log.info('Retrieving genes')
genes = {}
for genes_file in genes_files:
with open(genes_file,'r') as f:
genes[os.path.basename(genes_file)] = json.load(f)
gwas_result = None
_,input_ext = os.path.splitext(gwas_file)
log.info('Opening GWAS file')
if input_ext == '.csv':
gwas_result = result.load_from_csv(gwas_file)
else:
gwas_result = result.load_from_hdf5(gwas_file)
log.info('Loading genotype file')
genotype_data = _load_genotype_(genotype_folder)
top_snps = gwas_result.get_top_snps(args['top_snps_count'])
top_snps.sort(order=['scores'])
top_snps = top_snps[:args['top_snps_count']]
pval = enrichment.enrichment(genes,genotype_data,top_snps,args['window_size'],args['permutation_count'])
print json.dumps(pval)
return pval
def plot(args):
_, ext = os.path.splitext(args['file'])
if ext not in SUPPORTED_FILE_EXT:
raise Exception(
'The input file must have one of the supported extensions: %s' %
str(SUPPORTED_FILE_EXT))
chrs = None
marker_size = args['marker_size']
if 'chr' in args and args['chr'] is not None and args['chr'] != '':
chrs = [args['chr']]
gwas_result = None
if ext in HDF5_FILE_EXT:
gwas_result = result.load_from_hdf5(args['file'])
else:
gwas_result = result.load_from_csv(args['file'])
fdr = args['fdr']
colored = args['colored']
color_map = None
if colored:
color_map = ['b', 'g', 'r', 'c', 'm']
plotting.plot_gwas_result(gwas_result,
args['output'],
chrs,
args['macs'],
marker_size=marker_size,
fdr=fdr,
color_map=color_map)
def calc_ld(args):
positions = args['positions']
range = int(args['range'])
is_chr_pos = CHR_POS_PATTERN.match(positions)
genotypeData = genotype.load_hdf5_genotype_data(args['genotype_file'])
accession_file = args.get('acession_file',None)
if accession_file is not None:
accessions = _load_accessions(accession_file)
genotypeData.filter_accessions(accessions)
genotypeData.filter_non_binary()
if is_chr_pos:
chr = is_chr_pos.group(1)
position = int(is_chr_pos.group(2))
log.info('Calculating LD for chr %s and position %s with +/- range of %s' % (chr,position, range))
# get the positions
abs_ix,ix,found = genotypeData.get_pos_ix(chr,position)
min_ix = max(0,abs_ix - range)
max_ix = min(abs_ix + range, genotypeData.genome_length)
chr_pos_list = zip(genotypeData.chromosomes[min_ix:max_ix],genotypeData.positions[min_ix:max_ix])
else:
if os.path.exists(positions) == False:
raise ValueError('%s path does not exist' % positions)
# get the SNPs
_,ext = os.path.splitext(positions)
if ext not in SUPPORTED_FILE_EXT:
raise Exception('The input file must have one of the supported extensions: %s' % str(SUPPORTED_FILE_EXT))
if ext in HDF5_FILE_EXT:
gwas_result = result.load_from_hdf5(positions)
else:
gwas_result = result.load_from_csv(positions)
gwas_data = gwas_result.get_top_snps(range)
chr_pos_list = zip(map(str,gwas_data['chr']),gwas_data['positions'])
chr_pos_list = sorted(chr_pos_list,key=itemgetter(0,1))
ld_data = genotypeData.calculate_ld(chr_pos_list)
_save_ld_data(args['output_file'],ld_data,chr_pos_list)
def qq_plot(args):
_,ext = os.path.splitext(args['file'])
if ext not in SUPPORTED_FILE_EXT:
raise Exception('The input file must have one of the supported extensions: %s' % str(SUPPORTED_FILE_EXT))
gwas_result = None
if ext in HDF5_FILE_EXT:
gwas_result = result.load_from_hdf5(args['file'])
else:
gwas_result = result.load_from_csv(args['file'])
plotting.plot_qq(gwas_result,args['output'])
def qq_plot(args):
_, ext = os.path.splitext(args['file'])
if ext not in SUPPORTED_FILE_EXT:
raise Exception(
'The input file must have one of the supported extensions: %s' %
str(SUPPORTED_FILE_EXT))
gwas_result = None
if ext in HDF5_FILE_EXT:
gwas_result = result.load_from_hdf5(args['file'])
else:
gwas_result = result.load_from_csv(args['file'])
plotting.plot_qq(gwas_result, args['output'])
def convert(args):
_,input_ext = os.path.splitext(args['inputfile'])
_,output_ext = os.path.splitext(args['outputfile'])
if input_ext == output_ext:
raise Exception('use different file extension for input (%s) and output file (%s)' % (input_ext,output_ext))
if input_ext not in SUPPORTED_FILE_EXT:
raise Exception('The input file must have one of the supported extensions: %s' % str(SUPPORTED_FILE_EXT))
if output_ext not in SUPPORTED_FILE_EXT:
raise Exception('The output file must have one of the supported extensions: (%s)' % ', '.join(SUPPORTED_FILE_EXT))
gwas_result = None
if input_ext == '.csv':
gwas_result = result.load_from_csv(args['inputfile'])
gwas_result.save_as_hdf5(args['outputfile'])
else:
gwas_result = result.load_from_hdf5(args['inputfile'])
gwas_result.save_as_csv(args['outputfile'])
def plot(args):
_,ext = os.path.splitext(args['file'])
if ext not in SUPPORTED_FILE_EXT:
raise Exception('The input file must have one of the supported extensions: %s' % str(SUPPORTED_FILE_EXT))
chrs = None
marker_size = args['marker_size']
if 'chr' in args and args['chr'] is not None and args['chr'] != '':
chrs = [args['chr']]
gwas_result = None
if ext in HDF5_FILE_EXT:
gwas_result = result.load_from_hdf5(args['file'])
else:
gwas_result = result.load_from_csv(args['file'])
fdr = args['fdr']
colored = args['colored']
color_map = None
if colored:
color_map = ['b', 'g', 'r', 'c', 'm']
plotting.plot_gwas_result(gwas_result,args['output'],chrs,args['macs'],marker_size=marker_size, fdr=fdr, color_map=color_map)
def calc_ld(args):
positions = args['positions']
range = int(args['range'])
is_chr_pos = CHR_POS_PATTERN.match(positions)
genotypeData = genotype.load_hdf5_genotype_data(args['genotype_file'])
accession_file = args.get('acession_file', None)
if accession_file is not None:
accessions = _load_accessions(accession_file)
genotypeData.filter_accessions(accessions)
genotypeData.filter_non_binary()
if is_chr_pos:
chr = is_chr_pos.group(1)
position = int(is_chr_pos.group(2))
log.info(
'Calculating LD for chr %s and position %s with +/- range of %s' %
(chr, position, range))
# get the positions
abs_ix, ix, found = genotypeData.get_pos_ix(chr, position)
min_ix = max(0, abs_ix - range)
max_ix = min(abs_ix + range, genotypeData.genome_length)
chr_pos_list = zip(genotypeData.chromosomes[min_ix:max_ix],
genotypeData.positions[min_ix:max_ix])
else:
if os.path.exists(positions) == False:
raise ValueError('%s path does not exist' % positions)
# get the SNPs
_, ext = os.path.splitext(positions)
if ext not in SUPPORTED_FILE_EXT:
raise Exception(
'The input file must have one of the supported extensions: %s'
% str(SUPPORTED_FILE_EXT))
if ext in HDF5_FILE_EXT:
gwas_result = result.load_from_hdf5(positions)
else:
gwas_result = result.load_from_csv(positions)
gwas_data = gwas_result.get_top_snps(range)
chr_pos_list = zip(map(str, gwas_data['chr']), gwas_data['positions'])
chr_pos_list = sorted(chr_pos_list, key=itemgetter(0, 1))
ld_data = genotypeData.calculate_ld(chr_pos_list)
_save_ld_data(args['output_file'], ld_data, chr_pos_list)
def convert(args):
_, input_ext = os.path.splitext(args['inputfile'])
_, output_ext = os.path.splitext(args['outputfile'])
if input_ext == output_ext:
raise Exception(
'use different file extension for input (%s) and output file (%s)'
% (input_ext, output_ext))
if input_ext not in SUPPORTED_FILE_EXT:
raise Exception(
'The input file must have one of the supported extensions: %s' %
str(SUPPORTED_FILE_EXT))
if output_ext not in SUPPORTED_FILE_EXT:
raise Exception(
'The output file must have one of the supported extensions: (%s)' %
', '.join(SUPPORTED_FILE_EXT))
gwas_result = None
if input_ext == '.csv':
gwas_result = result.load_from_csv(args['inputfile'])
gwas_result.save_as_hdf5(args['outputfile'])
else:
gwas_result = result.load_from_hdf5(args['inputfile'])
gwas_result.save_as_csv(args['outputfile'])
