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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,125 @@ | ||
| import pandas as pd | ||
| import numpy as np | ||
| import allel | ||
| import snpmatch | ||
| import logging | ||
| import os | ||
| import json | ||
|
|
||
| log = logging.getLogger(__name__) | ||
|
|
||
| def parseGT(snpGT): | ||
| first = snpGT[0] | ||
| snpBinary = np.zeros(len(snpGT), dtype = "int8") | ||
| if first.find('|') != -1: | ||
| ## GT is phased | ||
| separator = "|" | ||
| elif first.find('/') != -1: | ||
| ## GT is not phased | ||
| separator = "/" | ||
| elif np.char.isdigit(first): | ||
| return np.array(np.copy(snpGT), dtype = "int8") | ||
| else: | ||
| snpmatch.die("unable to parse the format of GT in vcf!") | ||
| hetGT = "0" + separator + "1" | ||
| refGT = "0" + separator + "0" | ||
| altGT = "1" + separator + "1" | ||
| nocall = "." + separator + "." | ||
| snpBinary[np.where(snpGT == altGT)[0]] = 1 | ||
| snpBinary[np.where(snpGT == hetGT)[0]] = 2 | ||
| snpBinary[np.where(snpGT == nocall)[0]] = -1 | ||
| return snpBinary | ||
|
|
||
| def parseChrName(targetCHR): | ||
| snpCHROM = np.char.replace(np.core.defchararray.lower(np.array(targetCHR, dtype="string")), "chr", "") | ||
| snpsREQ = np.where(np.char.isdigit(snpCHROM))[0] ## Filtering positions from mitochondrial and chloroplast | ||
| snpCHR = snpCHROM[snpsREQ] | ||
| return (snpCHR, snpsREQ) | ||
|
|
||
| def readBED(inFile, logDebug): | ||
| log.info("reading the position file") | ||
| targetSNPs = pd.read_table(inFile, header=None, usecols=[0,1,2]) | ||
| (snpCHR, snpsREQ) = parseChrName(targetSNPs[0]) | ||
| snpPOS = np.array(targetSNPs[1], dtype=int)[snpsREQ] | ||
| snpGT = np.array(targetSNPs[2])[snpsREQ] | ||
| snpBinary = parseGT(snpGT) | ||
| snpWEI = np.ones((len(snpCHR), 3)) ## for homo and het | ||
| snpWEI[np.where(snpBinary != 0),0] = 0 | ||
| snpWEI[np.where(snpBinary != 1),2] = 0 | ||
| snpWEI[np.where(snpBinary != 2),1] = 0 | ||
| return (snpCHR, snpPOS, snpGT, snpWEI) | ||
|
|
||
| def readVcf(inFile, logDebug): | ||
| log.info("reading the VCF file") | ||
| ## We read only one sample from the VCF file | ||
| if logDebug: | ||
| vcf = allel.read_vcf(inFile, samples = [0], fields = '*') | ||
| else: | ||
| import StringIO | ||
| import sys | ||
| sys.stderr = StringIO.StringIO() | ||
| vcf = allel.read_vcf(inFile, samples = [0], fields = '*') | ||
| #vcf = vcfnp.variants(inFile, cache=False).view(np.recarray) | ||
| #vcfD = vcfnp.calldata_2d(inFile, cache=False).view(np.recarray) | ||
| sys.stderr = sys.__stderr__ | ||
| (snpCHR, snpsREQ) = parseChrName(vcf['variants/CHROM']) | ||
| try: | ||
| snpGT = allel.GenotypeArray(vcf['calldata/GT']).to_gt()[snpsREQ, 0] | ||
| except AttributeError: | ||
| snpmatch.die("input VCF file doesnt have required GT field") | ||
| snpsREQ = snpsREQ[np.where(snpGT != './.')[0]] | ||
| snpGT = allel.GenotypeArray(vcf['calldata/GT']).to_gt()[snpsREQ, 0] | ||
| if 'calldata/PL' in sorted(vcf.keys()): | ||
| snpWEI = np.copy(vcf['calldata/PL'][snpsREQ, 0]).astype('float') | ||
| snpWEI = snpWEI/(-10) | ||
| snpWEI = np.exp(snpWEI) | ||
|
|
||
| else: | ||
| snpBinary = parseGT(snpGT) | ||
| snpWEI = np.ones((len(snpsREQ), 3)) ## for homo and het | ||
| snpWEI[np.where(snpBinary != 0),0] = 0 | ||
| snpWEI[np.where(snpBinary != 1),2] = 0 | ||
| snpWEI[np.where(snpBinary != 2),1] = 0 | ||
| snpCHR = snpCHR[snpsREQ] | ||
| DPmean = np.mean(vcf['calldata/DP'][snpsREQ,0]) | ||
| snpPOS = np.array(vcf['variants/POS'][snpsREQ]) | ||
| return (DPmean, snpCHR, snpPOS, snpGT, snpWEI) | ||
|
|
||
| def parseInput(inFile, logDebug, outFile = "parser"): | ||
| if outFile == "parser" or not outFile: | ||
| outFile = inFile + ".snpmatch" | ||
| if os.path.isfile(inFile + ".snpmatch.npz"): | ||
| log.info("snpmatch parser dump found! loading %s", inFile + ".snpmatch.npz") | ||
| snps = np.load(inFile + ".snpmatch.npz") | ||
| (snpCHR, snpPOS, snpGT, snpWEI, DPmean) = (snps['chr'], snps['pos'], snps['gt'], snps['wei'], snps['dp']) | ||
| else: | ||
| _,inType = os.path.splitext(inFile) | ||
| if inType == '.npz': | ||
| log.info("loading snpmatch parser file! %s", inFile) | ||
| snps = np.load(inFile) | ||
| (snpCHR, snpPOS, snpGT, snpWEI, DPmean) = (snps['chr'], snps['pos'], snps['gt'], snps['wei'], snps['dp']) | ||
| else: | ||
| log.info('running snpmatch parser!') | ||
| if inType == '.vcf': | ||
| (DPmean, snpCHR, snpPOS, snpGT, snpWEI) = readVcf(inFile, logDebug) | ||
| elif inType == '.bed': | ||
| (snpCHR, snpPOS, snpGT, snpWEI) = readBED(inFile, logDebug) | ||
| DPmean = "NA" | ||
| else: | ||
| snpmatch.die("input file type %s not supported" % inType) | ||
| log.info("creating snpmatch parser file: %s", outFile + '.npz') | ||
| np.savez(outFile, chr = snpCHR, pos = snpPOS, gt = snpGT, wei = snpWEI, dp = DPmean) | ||
| NumSNPs = len(snpCHR) | ||
| case = 0 | ||
| note = "Sufficient number of SNPs" | ||
| if NumSNPs < snpmatch.snp_thres: | ||
| note = "Attention: low number of SNPs provided" | ||
| case = 1 | ||
| snpst = np.unique(snpCHR, return_counts=True) | ||
| snpdict = dict(('Chr%s' % snpst[0][i], snpst[1][i]) for i in range(len(snpst[0]))) | ||
| statdict = {"interpretation": {"case": case, "text": note}, "snps": snpdict, "num_of_snps": NumSNPs, "depth": DPmean} | ||
| statdict['percent_heterozygosity'] = snpmatch.getHeterozygosity(snpGT) | ||
| with open(outFile + ".stats.json", "w") as out_stats: | ||
| out_stats.write(json.dumps(statdict)) | ||
| log.info("done!") | ||
| return (snpCHR, snpPOS, snpGT, snpWEI, DPmean) |
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