def predictMutations(theta_file, target_seq, pam_idx, add_null=True):
theta, train_set, theta_feature_columns = readTheta(theta_file)
#generate indels
left_trim = 0
tmp_genindels_file = 'tmp_genindels_%s_%d.txt' % (target_seq, random.randint(0,100000))
cmd = INDELGENTARGET_EXE + ' %s %d %s' % (target_seq, pam_idx, tmp_genindels_file)
print(cmd); subprocess.check_call(cmd.split())
rep_reads = fetchRepReads(tmp_genindels_file)
isize, smallest_indel = min([(tokFullIndel(x)[1],x) for x in rep_reads]) if len(rep_reads) > 0 else (0,'-')
if isize > 0: left_trim = target_seq.find(rep_reads[smallest_indel][:10])
#compute features for all generated indels
tmp_features_file = 'tmp_features_%s_%d.txt' % (target_seq, random.randint(0,100000))
calculateFeaturesForGenIndelFile( tmp_genindels_file, target_seq, pam_idx-3, tmp_features_file)
os.remove(tmp_genindels_file)
feature_data, feature_columns = readFeaturesData(tmp_features_file)
os.remove(tmp_features_file)
if len(set(theta_feature_columns).difference(set(feature_columns))) != 0:
raise Exception('Stored feature names associated with model thetas are not contained in those computed')
if len(set(theta_feature_columns).union(set(feature_columns))) != len(theta_feature_columns):
feature_data = feature_data[['Indel'] + theta_feature_columns]
feature_columns = theta_feature_columns
#Predict the profile
p_predict, _ = computePredictedProfile(feature_data, theta, theta_feature_columns)
in_frame, out_frame, _ = fetchIndelSizeCounts(p_predict)
in_frame_perc = in_frame*100.0/(in_frame + out_frame)
if add_null:
p_predict['-'] = 1000
rep_reads['-'] = target_seq[left_trim:]
return p_predict, rep_reads, in_frame_perc
def computePercAbove30(profile):
above_count, below_count = 0, 0
i, o, s = fetchIndelSizeCounts(profile)
for x in s['D']:
if x > 30:
above_count += s['D'][x]
else:
below_count += s['D'][x]
count_i = 0
for x in s['I']:
count_i += s['I'][x]
return above_count * 100.0 / (below_count + above_count + count_i)
def getInFramePerc(profile):
p_if, p_of, _ = fetchIndelSizeCounts(profile)
p_if_perc = p_if * 100.0 / (p_if + p_of)
return p_if_perc
def compareOverbeekProfiles(
selected_overbeek_id=None,
pred_results_dir='../indel_prediction/model_testing'):
new_dirs = [
'ST_June_2017/data/K562_800x_LV7A_DPI7/mapped_reads/Oligos_71',
'ST_June_2017/data/K562_800x_LV7A_DPI10/mapped_reads/Oligos_71',
'ST_June_2017/data/K562_800x_LV7B_DPI7/mapped_reads/Oligos_71',
'ST_June_2017/data/K562_800x_LV7B_DPI10/mapped_reads/Oligos_71',
'ST_June_2017/data/K562_1600x_LV7B_DPI5/mapped_reads/Oligos_71',
'ST_Feb_2018/data/CAS9_12NA_1600X_DPI7/mapped_reads/Oligos_71'
]
#Old Samples
old_dirs = [
'ST_June_2017/data/K562_1600x_6OA_DPI5/mapped_reads/Oligos_71',
'ST_June_2017/data/K562_1600x_6OA_DPI7/mapped_reads/Oligos_71',
'ST_April_2017/data/K562_800x_6OA_DPI3_Old7/mapped_reads/Oligos_71',
'ST_April_2017/data/K562_800x_6OA_DPI7_Old8/mapped_reads/Oligos_71',
'ST_April_2017/data/K562_800x_6OA_DPI10_Old9/mapped_reads/Oligos_71',
'ST_April_2017/data/K562_800x_6OB_DPI3_Old10/mapped_reads/Oligos_71',
'ST_April_2017/data/K562_800x_6OB_DPI7_Old11/mapped_reads/Oligos_71',
'ST_April_2017/data/K562_800x_6OB_DPI10_Old12/mapped_reads/Oligos_71'
]
remove_long_indels = False
remove_wt, wt_thresh = True, 3.0
mappings = loadMappings()
all_overbeek_profiles, all_new_profiles, all_old_profiles, all_our_profiles, sel_overbeek_ids,oldnew_overbeek_ids, old_ids, new_ids = [],[],[],[], [],[],[],[]
overbeek_inframes, ours_inframes, oof_sel_overbeek_ids = [], [], []
kls, kls_old, kls_new, log_reads, overbeek_ids, above30_percentages, log_reads_new, log_reads_old, min_log_reads = [],[],[],[],[],[],[],[], []
for idx in range(1, 97):
overbeek_id = 'Overbeek%d' % idx
if selected_overbeek_id is not None and selected_overbeek_id != overbeek_id:
continue
if overbeek_id not in mappings:
continue
overbeek_filename = getHighDataDir(
) + '/overbeek_fastq_files/' + overbeek_id + '_mappedindelsummary.txt'
p1, p1_new, p1_old, o1, rep_reads1, rep_reads2 = {}, {}, {}, {}, {}, {}
nreads2, nreads1, nreads_old, nreads_new, nnull_old, nnull_new, nnull1, nnull2 = 0, 0, 0, 0, 0, 0, 0, 0
#Read the overbreek profile
numread2, perc_accept2, num_null2 = readSummaryToProfile(
overbeek_filename,
o1,
oligoid=overbeek_id,
remove_long_indels=remove_long_indels,
remove_wt=False)
if selected_overbeek_id is not None:
fetchRepresentativeCleanReads(
getHighDataDir() + '/overbeek_fastq_files/' + overbeek_id +
'_mappedindelprofiles.txt',
rep_reads2,
oligoid=overbeek_id)
pam_loc2, pam_dir2 = getNullTargetPamDetails(
getHighDataDir() + '/overbeek_control_fastq_files/' +
overbeek_id + '_exptargets.txt',
oligoid=overbeek_id)
nreads2 += numread2
nnull2 += num_null2
if numread2 == 0: continue
p1_new_reps, p1_old_reps = [{}, {}], [{}, {}]
rr_new_reps, rr_old_reps = [{}, {}], [{}, {}]
#Read all the new and old profiles
pam_loc1, pam_dir1 = None, None
for oligo_id, is_old in mappings[overbeek_id]:
#Read all reads for all our K562 profiles
oligo_idx = eval(oligo_id[5:])
_, oligo_fileprefix = getFileForOligoIdx(oligo_idx, ext='')
oligo_filename = oligo_fileprefix + '_mappedindelsummary.txt'
read_filename = oligo_fileprefix + '_mappedindelprofiles.txt'
exptarget_filename = oligo_fileprefix + '_exptargets.txt'
if is_old:
oligo_dirs, p1_old_new, null_oligo_dir = old_dirs, p1_old, 'ST_April_2017/data/NULL_Old/mapped_reads/Oligos_71'
p1_reps, rr_reps = p1_old_reps, rr_old_reps
else:
oligo_dirs, p1_old_new, null_oligo_dir = new_dirs, p1_new, 'ST_April_2017/data/NULL_New/mapped_reads/Oligos_71'
p1_reps, rr_reps = p1_new_reps, rr_new_reps
for oligo_dir in [getHighDataDir() + '/' + x for x in oligo_dirs]:
nr1, pa1, nn1 = readSummaryToProfile(
oligo_dir + '/' + oligo_filename,
p1_old_new,
oligoid=oligo_id,
remove_long_indels=remove_long_indels,
remove_wt=remove_wt,
wt_thresh=wt_thresh)
numread1, perc_accept1, num_null1 = readSummaryToProfile(
oligo_dir + '/' + oligo_filename,
p1,
oligoid=oligo_id,
remove_long_indels=remove_long_indels,
remove_wt=remove_wt,
wt_thresh=wt_thresh)
if 'DPI7' in oligo_dir:
rep_idx = 0 if '800x' in oligo_dir else 1
nr_rep, pa_rep, nn_rep = readSummaryToProfile(
oligo_dir + '/' + oligo_filename,
p1_reps[rep_idx],
oligoid=oligo_id,
remove_long_indels=remove_long_indels,
remove_wt=remove_wt,
wt_thresh=wt_thresh)
if selected_overbeek_id is not None:
fetchRepresentativeCleanReads(oligo_dir + '/' +
read_filename,
rep_reads1,
oligoid=oligo_id)
if 'DPI7' in oligo_dir:
fetchRepresentativeCleanReads(oligo_dir + '/' +
read_filename,
rr_reps[rep_idx],
oligoid=oligo_id)
if pam_loc1 is None:
pam_loc1, pam_dir1 = getNullTargetPamDetails(
getHighDataDir() + '/' + null_oligo_dir + '/' +
exptarget_filename,
oligoid=oligo_id)
if is_old:
nreads_old += numread1
nnull_old += num_null1
else:
nreads_new += numread1
nnull_new += num_null1
nreads1 += numread1
nnull1 += num_null1
kls.append(symmetricKL(p1, o1, True))
kls_old.append(symmetricKL(p1_old, o1, True))
kls_new.append(symmetricKL(p1_new, o1, True))
log_reads.append(np.log10(nreads1 - nnull1 + 0.5))
log_reads_old.append(np.log10(nreads_old - nnull_old + 0.5))
log_reads_new.append(np.log10(nreads_new - nnull_new + 0.5))
min_log_reads.append(min(log_reads_old[-1], log_reads_new[-1]))
above30_percentages.append(computePercAbove30(o1))
overbeek_ids.append(overbeek_id)
if log_reads[-1] > 2.0:
all_overbeek_profiles.append(o1)
all_our_profiles.append(p1)
sel_overbeek_ids.append(overbeek_id[8:])
if above30_percentages[-1] < 50.0:
oif, oof, _ = fetchIndelSizeCounts(o1)
pif, pof, _ = fetchIndelSizeCounts(p1)
overbeek_inframes.append(oif * 100.0 / (oif + oof))
ours_inframes.append(pif * 100.0 / (pif + pof))
oof_sel_overbeek_ids.append(overbeek_id)
if min_log_reads[-1] > 2.0:
all_new_profiles.append(p1_new)
all_old_profiles.append(p1_old)
oldnew_overbeek_ids.append(overbeek_id)
old_ids.append(
[id for id, is_old in mappings[overbeek_id] if is_old][0])
new_ids.append(
[id for id, is_old in mappings[overbeek_id] if not is_old][0])
try:
print(overbeek_id, [x for (x, y) in mappings[overbeek_id]],
kls[-1], nreads2, nreads1)
except KeyError:
print('Could not find', overbeek_id)
print(mappings)
if selected_overbeek_id is not None:
title = '%s (KL=%.1f)' % (overbeek_id, kls[-1])
labels = [
'Conventional scaffold Rep A', 'Conventional scaffold Rep B',
'Improved scaffold Rep A', 'Improved scaffold Rep B',
'Endogenous Profile'
]
plotProfiles([
p1_old_reps[0], p1_old_reps[1], p1_new_reps[0], p1_new_reps[0],
o1
], [
rr_old_reps[0], rr_old_reps[1], rr_new_reps[0], rr_new_reps[1],
rep_reads2
], [pam_loc1, pam_loc1, pam_loc1, pam_loc1, pam_loc2], [
x == 'REVERSE'
for x in [pam_dir1, pam_dir1, pam_dir1, pam_dir1, pam_dir2]
],
labels,
title=title)
if selected_overbeek_id is None:
plotInFrame(overbeek_inframes, ours_inframes, oof_sel_overbeek_ids,
pred_results_dir)
i = 1
PL.figure(figsize=(5.5, 5))
for thr_l, thr_h in [(0.0, 10.0), (10.0, 20.0), (20.0, 50.0),
(50.0, 90.0), (90.0, 100.0)]:
ydata = [
kl for (kl, a30, id, reads) in zip(kls, above30_percentages,
overbeek_ids, log_reads)
if a30 > thr_l and a30 <= thr_h
]
xdata = [
reads for (kl, a30, id, reads) in zip(kls, above30_percentages,
overbeek_ids, log_reads)
if a30 > thr_l and a30 <= thr_h
]
sel_ids = [
id for (kl, a30, id, reads) in zip(kls, above30_percentages,
overbeek_ids, log_reads)
if a30 > thr_l and a30 <= thr_h
]
PL.plot(xdata,
ydata,
'o',
label='%d-%d%% Deletions > 30' % (thr_l, thr_h))
for x, y, id in zip(xdata, ydata, sel_ids):
if y > 3 and x > 2:
PL.text(x, y, id)
PL.legend()
PL.plot([0, 6], [0.77, 0.77], '--', color='grey')
PL.text(0.1, 0.5, 'Median between our replicates', color='grey')
PL.ylabel('Symmetric KL Divergence', fontsize=12)
PL.xlabel('Log10 Mutated Reads', fontsize=12)
PL.xlim((0, 5.5))
PL.ylim((0, 8))
PL.show(block=False)
saveFig('scatter_KL')
i += 1
print('Median=', np.median(kls), 'Mean KL=', np.mean(kls))
print(len(overbeek_ids))
#Compute pairwise KL between overbeek and ours
N = len(sel_overbeek_ids)
kl_mat = np.zeros((N, N))
for i, o1 in enumerate(all_overbeek_profiles):
for j, p1 in enumerate(all_our_profiles):
kl_mat[i, j] = symmetricKL(o1, p1)
PL.figure(figsize=(8, 6))
PL.imshow(kl_mat,
cmap='hot_r',
vmin=0.0,
vmax=3.0,
interpolation='nearest')
PL.xticks(range(N), sel_overbeek_ids, rotation='vertical', fontsize=6)
PL.yticks(range(N),
sel_overbeek_ids,
rotation='horizontal',
fontsize=6)
PL.xlabel('Synthetic Measurement', fontsize=12)
PL.ylabel('Endogenous Measurement', fontsize=12)
PL.title('KL', fontsize=12)
PL.colorbar()
PL.show(block=False)
saveFig('heatmap_KL')
random.shuffle(alt2_id_pairs)
print(len(id_pairs), len(alt_id_pairs), len(alt2_id_pairs))
for (old_id, new_id), (alt_old_id,
alt_new_id), (alt2_old_id, alt2_new_id) in zip(
id_pairs, alt_id_pairs, alt2_id_pairs):
print(old_id, new_id)
p_old, p_new, mut_reads_old, mut_reads_new = loadProfilePair(
old_id, new_id)
old_ps, new_ps = loadSeparateProfilePairs(old_id, new_id)
p_old_alt, p_new_alt, mut_reads_old_alt, mut_reads_new_alt = loadProfilePair(
alt_old_id, alt_new_id)
p_old_alt2, p_new_alt2, mut_reads_old_alt2, mut_reads_new_alt2 = loadProfilePair(
alt2_old_id, alt2_new_id)
old_if, old_of, _ = fetchIndelSizeCounts(p_old)
new_if, new_of, _ = fetchIndelSizeCounts(p_new)
old_if_perc = old_if * 100.0 / (old_if + old_of)
new_if_perc = new_if * 100.0 / (new_if + new_of)
out_str = ''
for kl_func in [symmetricKL, classSymmetricKL]:
str_args = (kl_func(p_old,
p_new), meanSymKL(old_ps, kl_func=kl_func),
meanSymKL(new_ps, kl_func=kl_func))
out_str += u'\t%.5f\t%.5f\t%.5f' % str_args
out_str += u'\t%s\t%s\t%d\t%d' % (alt_old_id, alt_new_id,
mut_reads_old_alt, mut_reads_new_alt)
for kl_func in [symmetricKL, classSymmetricKL]:
str_args = (np.mean([
kl_func(p_old, p_new_alt),
def computeAndComparePredicted(theta_file, selected_id=None, out_dir='.'):
features_dir = getHighDataDir() + '/gen_indels/features_for_gen_indels'
theta, train_set, feature_columns = readTheta(theta_file)
#Note: here old refers to conventional scaffold library, new refers to improved scaffold library
fout = io.open(out_dir + '/old_new_kl_predicted_summaries.txt', 'w')
fout.write(
u'Old Oligo Id\tNew Oligo Id\tOld Mut Reads\tNew Mut Reads\tCombined Mut Reads\tOld In Frame Perc\tNew In Frame Perc\tCombined in Frame Perc\tPredicted In Frame Per'
)
fout.write(
u'\tOld v New KL\tOld v Predicted KL\tNew v Predicted KL\tCombined v Predicted KL\n'
)
id_pairs = loadValidationPairs()
for (old_id, new_id) in id_pairs:
if old_id in train_set or new_id in train_set:
raise Exception('Bad!!! Testing on Training data: %s %s' %
(old_id, new_id))
if selected_id is not None and selected_id != old_id:
continue #Guide pair selected for plotting
#Load Old and new profiles, and produce combined profile from the two
p_old, p_new, mut_reads_old, mut_reads_new = loadProfilePair(
old_id, new_id)
p_comb, mut_reads_comb = combineProfiles(p_old, p_new, mut_reads_old,
mut_reads_new)
#Predict the profile (old and new will be the same so just do one)
feature_data = loadOligoFeaturesAndReadCounts(new_id, [])
p_predict, _ = computePredictedProfile(feature_data, theta,
feature_columns)
#Compute in frame percentages
old_if, old_of, _ = fetchIndelSizeCounts(p_old)
new_if, new_of, _ = fetchIndelSizeCounts(p_new)
comb_if, comb_of, _ = fetchIndelSizeCounts(p_comb)
pred_if, pred_of, _ = fetchIndelSizeCounts(p_predict)
old_if_perc = old_if * 100.0 / (old_if + old_of)
new_if_perc = new_if * 100.0 / (new_if + new_of)
comb_if_perc = comb_if * 100.0 / (comb_if + comb_of)
pred_if_perc = pred_if * 100.0 / (pred_if + pred_of)
#Plot the comparison
if selected_id is not None:
rrds = loadRepReads(new_id)
plotProfiles([p_old, p_new, p_predict], [rrds, rrds, rrds],
[42, 42, 42], [False, False, False],
['Replicate 1', 'Replicate 2', 'Predicted'],
title='%s (KL=%.2f, KL=%.2f)' %
(new_id, symmetricKL(
p_old, p_new), symmetricKL(p_comb, p_predict)))
str_args = (symmetricKL(p_old, p_new), symmetricKL(p_old, p_predict),
symmetricKL(p_new,
p_predict), symmetricKL(p_comb, p_predict))
kl_str = u'\t%.5f\t%.5f\t%.5f\t%.5f' % str_args
fout.write(
u'%s\t%s\t%d\t%d\t%d\t%.3f\t%.3f\t%.3f\t%.3f%s\n' %
(old_id, new_id, mut_reads_old, mut_reads_new, mut_reads_comb,
old_if_perc, new_if_perc, comb_if_perc, pred_if_perc, kl_str))
fout.flush()
fout.close()
