Skip to content

Commit

Permalink
Merge pull request #285 from /issues/284-fix-iars-without-normal-event
Browse files Browse the repository at this point in the history 
Fix event with inconsistency in normals with many IARS(resolves #284)
  • Loading branch information
@arkal
arkal authored May 18, 2018
2 parents 101565a + 3e195d9 commit 0631068
Showing 1 changed file with 34 additions and 30 deletions.
64 changes: 34 additions & 30 deletions src/protect/binding_prediction/common.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -329,7 +329,7 @@ def pept_diff(p1, p2):
return sum([p1[i] != p2[i] for i in range(len(p1))])


def _get_normal_peptides(mhc_df, iars, peplen):
def _get_normal_peptides(job, mhc_df, iars, peplen):
"""
Get the corresponding normal peptides for the tumor peptides that have already been subjected to
mhc:peptide binding prediction.
Expand All @@ -345,38 +345,42 @@ def _get_normal_peptides(mhc_df, iars, peplen):
for pred in mhc_df.itertuples():
containing_iars = [i for i, sl in iars.items() if pred.pept in sl[0]]
assert len(containing_iars) != 0, "No IARS contained the peptide"
if len(containing_iars) > 1:
# If there are multiple IARs, they all or none of them have to have a corresponding
# normal.
assert len(set([len(y) for x, y in iars.items() if x in containing_iars])) == 1
if len(iars[containing_iars[0]]) == 1:
# This is a fusion and has no corresponding normal
normal_peptides.append('N' * peplen)
else:
tum, norm = iars[containing_iars[0]]
pos = tum.find(pred.pept)
temp_normal_pept = norm[pos:pos + peplen]
ndiff = pept_diff(pred.pept, temp_normal_pept)
assert ndiff != 0
if ndiff == 1:
normal_peptides.append(norm[pos:pos + peplen])
# If there are multiple IARs, they all or none of them have to have a corresponding
# normal.
if len(set([len(y) for x, y in iars.items() if x in containing_iars])) != 1:
job.fileStore.logToMaster('Some IARS were found to contain the substring but were'
'inconsistent with the presence of a corresponding '
'normal.')
normal_peptides.append('N' * peplen)
else:
if len(tum) == len(norm):
# Too (2+) many single nucleotide changes to warrant having a normal counterpart
# This might be an artifact
normal_peptides.append('N' * peplen)
tum, norm = iars[containing_iars[0]]
pos = tum.find(pred.pept)
temp_normal_pept = norm[pos:pos + peplen]
ndiff = pept_diff(pred.pept, temp_normal_pept)
assert ndiff != 0
if ndiff == 1:
normal_peptides.append(norm[pos:pos + peplen])
else:
# There is an indel in play. The difference cannot be in the last AA as that
# would have come out properly in the first case. There is a possibility that
# the indel was in the first AA causing a shift. We can handle that by looking
# at the suffix.
pos = norm.find(pred.pept[1:])
if pos != -1:
# The suffix was found,
normal_peptides.append(norm[pos-1:pos + peplen])
else:
# The indel was too large to warrant having a normal counterpart
if len(tum) == len(norm):
# Too (2+) many single nucleotide changes to warrant having a normal
# counterpart. This might be an artifact
normal_peptides.append('N' * peplen)
else:
# There is an indel in play. The difference cannot be in the last AA as that
# would have come out properly in the first case. There is a possibility
# that the indel was in the first AA causing a shift. We can handle that by
# looking at the suffix.
pos = norm.find(pred.pept[1:])
if pos != -1:
# The suffix was found,
normal_peptides.append(norm[pos-1:pos + peplen])
else:
# The indel was too large to warrant having a normal counterpart
normal_peptides.append('N' * peplen)

mhc_df['normal_pept'] = normal_peptides
return mhc_df, normal_peptides
Expand Down Expand Up @@ -417,7 +421,7 @@ def predict_normal_binding(job, binding_result, transgened_files, allele, peplen
'predictor': None}
elif predictor == 'Consensus':
results = _process_consensus_mhcii(mhc_file)
results, peptides = _get_normal_peptides(results, iars, peplen)
results, peptides = _get_normal_peptides(job, results, iars, peplen)
with open('peptides.faa', 'w') as pfile:
for pept in peptides:
print('>', pept, '\n', pept, sep='', file=pfile)
Expand All @@ -431,7 +435,7 @@ def predict_normal_binding(job, binding_result, transgened_files, allele, peplen
'predictor': 'Consensus'}
elif predictor == 'Sturniolo':
results = _process_sturniolo_mhcii(mhc_file)
results, peptides = _get_normal_peptides(results, iars, peplen)
results, peptides = _get_normal_peptides(job, results, iars, peplen)
with open('peptides.faa', 'w') as pfile:
for pept in peptides:
print('>', pept, '\n', pept, sep='', file=pfile)
Expand All @@ -445,7 +449,7 @@ def predict_normal_binding(job, binding_result, transgened_files, allele, peplen
'predictor': 'Sturniolo'}
elif predictor == 'netMHCIIpan':
results = _process_net_mhcii(mhc_file)
results, peptides = _get_normal_peptides(results, iars, peplen)
results, peptides = _get_normal_peptides(job, results, iars, peplen)
with open('peptides.faa', 'w') as pfile:
for pept in peptides:
print('>', pept, '\n', pept, sep='', file=pfile)
Expand All @@ -465,7 +469,7 @@ def predict_normal_binding(job, binding_result, transgened_files, allele, peplen
mhc_file = job.fileStore.readGlobalFile(binding_result,
os.path.join(work_dir, 'mhci_results'))
results = _process_mhci(mhc_file)
results, peptides = _get_normal_peptides(results, iars, peplen)
results, peptides = _get_normal_peptides(job, results, iars, peplen)
with open('peptides.faa', 'w') as pfile:
for pept in peptides:
print('>', pept, '\n', pept, sep='', file=pfile)
Expand Down

0 comments on commit 0631068

Please sign in to comment.