def get_single_performance(region, outdir, method, debug=False):
sglfo = glutils.read_glfo(outdir + '/germlines/simulation', locus=args.locus)
iglfo = glutils.read_glfo(outdir + '/' + method + '/sw/germline-sets', locus=args.locus)
glutils.synchronize_glfos(ref_glfo=sglfo, new_glfo=iglfo, region=region)
missing_alleles = set(sglfo['seqs'][region]) - set(iglfo['seqs'][region])
spurious_alleles = set(iglfo['seqs'][region]) - set(sglfo['seqs'][region])
if debug:
if len(missing_alleles) > 0:
print ' %2d missing %s' % (len(missing_alleles), ' '.join([utils.color_gene(g) for g in missing_alleles]))
if len(spurious_alleles) > 0:
print ' %2d spurious %s' % (len(spurious_alleles), ' '.join([utils.color_gene(g) for g in spurious_alleles]))
if len(missing_alleles) == 0 and len(spurious_alleles) == 0:
print ' none missing'
return {
'missing' : len(missing_alleles),
'spurious' : len(spurious_alleles),
'total' : len([g for g in sglfo['seqs'][region] if '+' in g]), # anybody with a '+' should be a new allele
}
def get_gene_sets(glsfnames, glslabels, ref_label=None):
glfos = {}
for label, fname in zip(glslabels, glsfnames):
gldir = os.path.dirname(fname).replace('/' + args.locus, '')
glfos[label] = glutils.read_glfo(
gldir, args.locus
) # this is gonna fail for tigger since you only have the .fa
if ref_label is not None:
for label in [l for l in glslabels if l != ref_label]:
print ' syncronizing %s names to match %s' % (label, ref_label)
glutils.synchronize_glfos(ref_glfo=glfos[ref_label],
new_glfo=glfos[label],
region=args.region)
gl_sets = {
label:
{g: seq
for g, seq in glfos[label]['seqs'][args.region].items()}
for label in glfos
}
all_genes = {g: s for gls in gl_sets.values() for g, s in gls.items()}
return all_genes, gl_sets