def __init__(self, organism, params=None):
self.organism = organism[:]
if params is None:
self.params = tcr_distances.DistanceParams()
else:
self.params = copy.deepcopy(params)
self.rep_dists = tcr_distances.compute_all_v_region_distances(
organism, self.params)
p.flag('intrasubject_nbrdists')
p.multiword('clones_files').cast(lambda x: x.split())
p.multiword('dist_chains').cast(lambda x: x.split(
)).default('A B AB').described_as(
'The chains over which the distance calcn will be performed; default is all three ("A B AB")'
)
p.multiword('epitope_prefixes').cast(lambda x: x.split())
p.multiword('nbrdist_percentiles').cast(
lambda x: [int(val) for val in x.split()]).default(
"5 10 25") #"5 10 25 -1 -5 -10")
p.str('distance_params')
#internal legacy hack
new_nbrdists = not intrasubject_nbrdists
distance_params = tcr_distances.DistanceParams(config_string=distance_params)
if not clones_files:
assert clones_file
clones_files = [clones_file]
if not epitope_prefixes:
epitope_prefixes = [''] * len(clones_files)
assert len(epitope_prefixes) == len(clones_files)
print 'precomputing v-region distances'
rep_dists = tcr_distances.compute_all_v_region_distances(
organism, distance_params)
print 'done precomputing v-region distances'
def make_default_logo_svg_cmds(upper_left,
width,
height,
organism,
tcr_infos,
ab,
distance_params=None,
rep_dists=None,
add_fake_alleles=False,
show_full_cdr3=False):
# right now single-chain only
# returns cmds
assert ab in 'AB'
if distance_params is None:
distance_params = tcr_distances.DistanceParams(config_string=None)
if rep_dists is None:
#print 'precomputing v-region distances'
rep_dists = tcr_distances.compute_all_v_region_distances(
organism, distance_params)
#print 'done precomputing v-region distances'
util.assign_label_reps_and_colors_based_on_most_common_genes_in_repertoire(
tcr_infos, organism)
rep_colors = {}
for info in tcr_infos:
for vj in 'vj':
for abl in 'ab':
rep = info[vj + abl + '_label_rep']
color = info[vj + abl + '_label_rep_color']
rep_colors[rep] = color
tcrs = []
dist_tcrs = []
def add_fake_allele_info(x):
if '*' not in x:
return x + '*01'
else:
return x
for l in tcr_infos:
mouse = l['subject']
epitope = l['epitope']
cdr3a = l['cdr3a']
cdr3b = l['cdr3b']
## for computing distances
va_gene = l['va_gene']
ja_gene = l['ja_gene']
va_genes = l['va_genes'].split(';')
vb_gene = l['vb_gene']
jb_gene = l['jb_gene']
vb_genes = l['vb_genes'].split(';')
# add '*01' -- hacky!
if add_fake_alleles:
va_genes = map(add_fake_allele_info, va_genes)
vb_genes = map(add_fake_allele_info, vb_genes)
va_gene = add_fake_allele_info(va_gene)
ja_gene = add_fake_allele_info(ja_gene)
vb_gene = add_fake_allele_info(vb_gene)
jb_gene = add_fake_allele_info(jb_gene)
va_reps = frozenset(
(all_genes.all_genes[organism][x].rep for x in va_genes))
vb_reps = frozenset(
(all_genes.all_genes[organism][x].rep for x in vb_genes))
dist_tcrs.append([va_reps, vb_reps, cdr3a, cdr3b])
#all_info.append( l )
## note that we are using mm1 reps here that also dont have allele info
va_rep = l['va_label_rep']
ja_rep = l['ja_label_rep']
vb_rep = l['vb_label_rep']
jb_rep = l['jb_label_rep']
cdr3a_nucseq_src = ['V'] * (3 * len(cdr3a)) ## hack, unused
cdr3b_nucseq_src = ['V'] * (3 * len(cdr3b))
if junction_bars:
if ab == 'A':
a_junction_results = tcr_sampler.analyze_junction(
organism,
va_gene,
ja_gene,
cdr3a,
l['cdr3a_nucseq'].lower(),
return_cdr3_nucseq_src=True)
cdr3a_new_nucseq, cdr3a_protseq_masked, cdr3a_protseq_new_nucleotide_countstring,\
a_trims, a_inserts, cdr3a_nucseq_src = a_junction_results
elif ab == 'B':
b_junction_results = tcr_sampler.analyze_junction(
organism,
vb_gene,
jb_gene,
cdr3b,
l['cdr3b_nucseq'].lower(),
return_cdr3_nucseq_src=True)
cdr3b_new_nucseq, cdr3b_protseq_masked, cdr3b_protseq_new_nucleotide_countstring,\
b_trims, b_inserts, cdr3b_nucseq_src = b_junction_results
## try to distinguish between N before D and N after D
for i in range(len(cdr3b_nucseq_src)):
if cdr3b_nucseq_src[i] == 'N':
if cdr3b_nucseq_src[:i].count('D') == 0:
cdr3b_nucseq_src[i] = 'N1'
else:
cdr3b_nucseq_src[i] = 'N2'
assert len(cdr3a_nucseq_src) == 3 * len(cdr3a)
assert len(cdr3b_nucseq_src) == 3 * len(cdr3b)
#print cdr3b, cdr3b_nucseq_src
tcrs.append((mouse, va_rep, ja_rep, vb_rep, jb_rep, cdr3a, cdr3b,
cdr3a_nucseq_src, cdr3b_nucseq_src, l['clone_id']))
## compute distances, used in logo construction for picking the center tcr for aligning against
#print 'computing distances:',len(dist_tcrs)
chains = ab
all_dists = np.zeros((len(dist_tcrs), len(dist_tcrs)))
for i, t1 in enumerate(dist_tcrs):
for j in range(i + 1, len(dist_tcrs)):
dist = tcr_distances.compute_distance(t1, dist_tcrs[j], chains,
rep_dists, distance_params)
all_dists[i][j] = dist
all_dists[j][i] = dist
# now make the logo
members = range(len(tcrs))
scale_w = float(width) / default_width
scale_h = float(height) / default_height
# scale everything by our desired height, width
return make_tcr_logo(upper_left, tcrs, members, all_dists, ab, rep_colors,
scale_w * default_vj_logo_width,
scale_w * default_pwmplusgaps_width,
scale_w * default_xpad, scale_h * default_pwm_height,
scale_h * default_junction_bars_height,
scale_h * default_ypad, show_full_cdr3)