def genes(self, geneset, amount):
"""
Draw random genes, where set is the geneset name selected
and amount the number of new sets to be formed
"""
geneset_to_snp_mapping = common.map_geneset_to_snp(self.drawrandom.snpmapping)
if (geneset not in geneset_to_snp_mapping):
log.info("\n" + geneset + " is not known as a geneset name. Please check your data for correct geneset name.")
log.info(_get_terminated_time())
sys.exit()
#load number of genes in geneset by the mapping file
self.exclude_genes = set([ x["g"] for x in geneset_to_snp_mapping[geneset]])
ngenes = len(self.exclude_genes)
gene2snp = self._gene2snpmapping() #create gene to all SNP's mapping
all_genes = set(gene2snp.keys())
if(len(all_genes) <= (ngenes*amount)):
max = len(all_genes)/ngenes
log.info("\nYour sample of " + str(len(all_genes)) + " genes is too small to draw " + str(amount) + " random genesets of size " + str(ngenes))
log.info("\nMaximum number of independent gene-sets to draw (" + str(len(all_genes))+"/"+ str(ngenes) + "): " + str(max))
log.info(_get_terminated_time())
sys.exit()
log.info("\nSize of gene pool (--pool): " + str(len(all_genes)) + " unique genes")
log.info("\nThe geneset " + geneset + " contains " + str(ngenes) + " genes" )
log.info("\nMinimum size of gene pool needed to draw " + str(amount) + " gene-sets (" + str(ngenes) + "*" + str(amount) + "): " + str(ngenes*amount))
#exclude genes that are in the selected geneset
if (self.drawrandom.exclude):
all_genes = all_genes.difference(set(self.exclude_genes))
output_text = ""
for new_set_number in xrange(1, amount + 1):
setname = "Draw_" + str(new_set_number)
sampled_keys = random.sample(all_genes, ngenes)
for gene_as_key in sampled_keys:
output_text += '\n'.join([str(snp) + "\t" + str(gene_as_key) + \
"\t" + setname for snp in gene2snp[gene_as_key]])
output_text += '\n'
incl_or_excl = "excl" if self.drawrandom.exclude else "incl" #create correct filename
filename = "draws_ngenes.set.annot"
out = self.drawrandom.inoutput.save_text_to_filename(filename, output_text) #save file
log.info("\nSaved random draws on number of genes as " + out)
return(output_text)
def snp(self, geneset, amount, empp_file, plink, out):
"""
draw random snp, on number of neff snps in the .empp file, from an independent snp file (.prune.in). If this file is not
present, this file will be created within _create_indep_snp_file function.
"""
geneset_to_snp_mapping = common.map_geneset_to_snp(self.drawrandom.snpmapping)
if (geneset not in geneset_to_snp_mapping):
log.info("\n" + geneset + " is not known as a geneset name. Please check your data for correct geneset name.")
log.info(_get_terminated_time())
sys.exit()
self.exclude_snps = set([ x["s"] for x in geneset_to_snp_mapping[geneset]]) #drawsnps
try:
n_snp = _read_empp_results(empp_file)[geneset]
except ValueError:
log.info("geneset to select is not found in empp file")
log.info(_get_terminated_time())
sys.exit()
prunedin_file = str(os.path.abspath(os.path.curdir)) + "/" + out + ".prune.in" #get pruned.in file
prunedin = os.path.exists(prunedin_file)
if (prunedin == False): #create prune.in from file, if it does not excist
prunedin = self._create_indep_snp_file(plink)
else:
log.info ("\nUsing the pruned SNP set from " + prunedin_file)
prunedin = prunedin_file
allsnp_and_genes = common.getfile_handle(prunedin).readlines() #pylint: disable=E1103
length_genic = 0
length_nongenic = 0
for line in allsnp_and_genes:
line = line.rsplit('\t')
gene = line[1].rsplit()
if len(gene) is not 0:
length_genic += 1
else:
length_nongenic += 1
amount_allsnp_and_genes = len(allsnp_and_genes) - 1
#random_snp_text = "RS#\tGeneID\tDraw_#\n"
random_snp_text = ""
for new_group_number in xrange(1, amount + 1):
self.drawrandom.accessed = set()
setname = "Draw_" + str(new_group_number)
count = 0
while(count < n_snp):
random_snp_text += ("\t".join(self._get_random_snp(allsnp_and_genes, amount_allsnp_and_genes)))
random_snp_text += ("\t" + setname + "\n")
count = count + 1
inregion_text = "unknown_in_region"
if(self.inregion == "genic"):
inregion_text = "genic"
if amount*n_snp > length_genic:
log.info("\nWarning: pool of " + str(length_genic) + " SNPs located within genes is to small to draw " + \
str(amount) + " x " + str(n_snp) + " independent nEff SNPs!")
log.info(_get_terminated_time())
sys.exit()
else:
log.info("\nDrawing " + str(amount) + " x " + str(n_snp) + " nEff SNPs from a pool of " + \
str(length_genic) + " SNPs located within genes")
elif(self.inregion == "intergenic"):
inregion_text = "intergenic"
if amount*n_snp > length_nongenic:
log.info("\nWarning: pool of " + str(length_nongenic) + " SNPs located outside genes is to small to draw " + \
str(amount) + " x " + str(n_snp) + " independent nEff SNPs!")
log.info(_get_terminated_time())
sys.exit()
else:
log.info("\nDrawing " + str(amount) + " x " + str(n_snp) + " nEff SNPs from a pool of " + \
str(length_nongenic) + " SNPs located outside genes")
elif(self.inregion == "all"):
inregion_text = "all"
if amount*n_snp > len(allsnp_and_genes):
log.info("\nWarning: pool of " + str(len(allsnp_and_genes)) + " SNPs located in- and outside genes is to small to draw " + \
str(amount) + " x " + str(n_snp) + " independent nEff SNPs!")
log.info(_get_terminated_time())
sys.exit()
else:
log.info("\nDrawing " + str(amount) + " x " + str(n_snp) + " nEff SNPs from a pool of " + \
str(len(allsnp_and_genes)) + " SNPs located in- and outside genes")
incl_or_excl = "unknown"
if (self.drawrandom.exclude is False):
incl_or_excl = "incl"
elif (self.drawrandom.exclude is True):
incl_or_excl = "excl"
filename = "draws_neff_" + inregion_text + ".set.annot"
out = self.drawrandom.inoutput.save_text_to_filename(filename, random_snp_text) #save random snps file
log.info("\nSaved random draws on number of effective number of SNPS as " + out)
return(filename)
