ggv_sounds.py

#!/usr/local/bin/python3

'''
	Outputting audio representation of the 
		geography of a genetic variant (from 1000 Genomes)
'''

import argparse as arg
import subprocess as sp
import requests as req

'''
	Super-population definitions in 1000 Genomes
'''

AFR = ['YRI', 'LWK', 'GWD', 'MSL', 'ESN', 'ASW', 'ACB']
EUR = ['CEU', 'TSI', 'FIN', 'GBR', 'IBS']
SAS = ['GIH', 'PJL', 'BEB', 'STU', 'ITU']
EAS = ['CHB', 'JPT', 'CHS', 'CDX', 'KHV']
AMR = ['MXL', 'PUR', 'CLM', 'PEL']

superpops = ['Africa', 'Europe', 'South Asia', 'East Asia', 'Americas']

'''
	Extracts a variant via the ggv api
	@arg rsID : rsID of variant in 1000 genomes
	@return : json dictionary holding variant fields
'''
def get_variant(rsID=None):
	if rsID is None:
		snp = req.get("http://popgen.uchicago.edu/ggv_api/freq_table?data=%221000genomes_table%22&random_snp=True")
	else:
		snp = req.get("http://popgen.uchicago.edu/ggv_api/freq_table?data=%221000genomes_table%22&rsID=%s", rsID)
	return(snp.json())


'''
	Function to collect variant frequency in various populations
	@arg snp_json - json object from ggv api call
	@return - length 5 vector with super population frequencies
'''
def collect_freqs_superpops(snp_json):
	pop_dict = dict()
	pop = [snp_json[i]['pop'] for i in range(len(snp_json))]
	total_cnt = [(snp_json[i]['xobs'], snp_json[i]['nobs']) for i in range(len(snp_json))]
	for i in range(len(pop)):
		pop_dict[pop[i]] = total_cnt[i]
	# Assign superpopulation frequencies	
	AFR_freq = sum([float(pop_dict[i][0]) for i in AFR]) / sum([float(pop_dict[i][1]) for i in AFR])
	EUR_freq = sum([float(pop_dict[i][0]) for i in EUR]) / sum([float(pop_dict[i][1]) for i in EUR])
	EAS_freq = sum([float(pop_dict[i][0]) for i in EAS]) / sum([float(pop_dict[i][1]) for i in EAS])
	SAS_freq = sum([float(pop_dict[i][0]) for i in SAS]) / sum([float(pop_dict[i][1]) for i in SAS])
	AMR_freq = sum([float(pop_dict[i][0]) for i in AMR]) / sum([float(pop_dict[i][1]) for i in AMR])
	return([AFR_freq, EUR_freq, SAS_freq, EAS_freq, AMR_freq])


'''
	Categorization of one frequency (fancy binning)
	@arg frq - frequency of variant (0 <=  f <= 1)
	@arg rare - cutoff for calling something rare (def : 0.01)
	@arg low - cutoff for calling something low frequency (def : 0.05)
	@return - string categorizing variant frequency
'''
def categorize_freq(frq, rare = 0.01, low = 0.05):
	if frq == 0:
		return(None)
	elif frq > low:
		return('common')
	elif (frq < low) and (frq > rare):
		return('low-frequency')
	else:
		return('rare')

'''
	Heuristic Categorization of Variant Frequencies
	@arg superpop_freqs - length 5 vector of super pop frequencies
	@return - string representation of variant categorization
'''
def categorize_variant(superpop_freqs, rare = 0.01, low = 0.05):
	# s = ''
	if all([(frq > low) for frq in superpop_freqs]):
		s = 'globally common'
		return(s)
	elif all([ frq < low and frq > rare for frq in superpop_freqs]):
		s = 'globally low-frequency'
		return(s)
	elif all([frq < rare and frq > 0.0 for frq in superpop_freqs]):
		s = 'globally rare'
		return(s)
	else:
		s = ''
		for i in range(len(superpops)):
			cat = categorize_freq(superpop_freqs[i], rare, low)
			if (cat is not None):
				s += cat + ' in ' + superpops[i] + ','
		s = s[:-1]
	return(s)

'''
	Passing geodist to vocalization program
	@arg geodist string - description of geographic distribution of variant.
	@return - passes categorization to 'say' program
'''
def vocalize_geodist(geodist_str):
	sp.call(["say", geodist_str])


if __name__ =='__main__':
	# Parse all arguments given
	parser = arg.ArgumentParser()
	parser.add_argument('-r', '--rsID', type=str, required=False, help="rsID")
	args = parser.parse_args()

	#1. Get Json Object
	if args.rsID is not None:
		print('rsID : %s' % args.rsID)

	snp_json = get_variant(args.rsID)
	if len(snp_json) < 2:
		print('Incorrect formatting of rsID')
		exit(1)

	print('Chrom:Pos : %s' % snp_json[1]['chrom_pos'])


	#2. Get Super Population Frequencies
	superpop_freqs = collect_freqs_superpops(snp_json)
	print(superpop_freqs)

	#3. Get Variant Categorization
	geodist_string = categorize_variant(superpop_freqs)
	print(geodist_string)

	#4. Read off Geodist
	vocalize_geodist(geodist_string)