def generate_multi_mut_peptide(self):
max_mut = len(self.peptVarDict)
var_sets = []
for i in range(max_mut):
ids = list(itertools.combinations(self.peptVarDict.keys(), i + 1))
for idx in ids:
candidates = [self.peptVarDict[key] for key in idx]
var_sets.extend(list(itertools.product(*candidates)))
self.mut_pept = {}
for var_set in var_sets:
var_set_list = list(var_set)
var_set_list.sort(key=lambda x: x.pos)
var1_set = [var.var1 for var in var_set_list]
shifted_var_set = [
variant.shift_var(var.var1, self.start_pos)
for var in var_set_list
]
shifted_var_set = [
variant(self.pepID, var) for var in shifted_var_set
]
# shifted_var_set.sort(key = lambda x:x.pos) # sort variants based on ascending positions
self.mut_pept['_'.join(var1_set)] = self.multi_mutate(
shifted_var_set)
return
def generate_single_mut_peptide(self):
self.mut_pept = {}
for var in self.peptVariants:
shifted_var = variant.shift_var(var.var1, self.start_pos)
shifted_var = variant(self.pepID, shifted_var)
self.mut_pept[var.var1] = protein.mutate(self.seq, shifted_var)
return
def find_variants(self, variants, refSeq):
protVariants = variants[self.transcript]
self.peptVariants = []
for eachVar in protVariants:
var = variant(self.transcript, eachVar)
var.get_seq(refSeq)
if self.start_pos <= var.pos <= self.start_pos + self.length - 1:
if not var.is_RKP():
#self.peptVariants.append(var.var3)
self.peptVariants.append(var)
return
def build_protDB(refSeq_file, variants_file, output_dir, mut_only):
variants_read = cfunc.read_cmi_var(variants_file)
refSeq = cfunc.read_uniprotFa(refSeq_file)
# filter variants according to refSeq.
variants = {}
for key, var in variants_read.iteritems():
if key in refSeq.keys():
variants[key] = var
# Annotate proteins
print 'Annotating proteins and mutants...'
prot_profile = []
len_protein = 0
len_mutant = 0
for key in variants.keys():
eachProtein = refSeq[key]
protein1 = protein(eachProtein['header'], eachProtein['seq'])
prot_profile.append(protein1)
len_protein += 1
matchVariants = variants[protein1.transcript]
for var in matchVariants:
mprotein = protein(eachProtein['header'], eachProtein['seq'])
variant1 = variant(protein1.transcript, var)
mprotein.add_mutation(variant1)
prot_profile.append(mprotein)
len_mutant += 1
len_profile = len(prot_profile)
print 'Finished %d reference proteins.' % (len_protein)
print 'Finished %d mutant proteins.' % (len_mutant)
print 'Annotated %d peptides.\n' % (len_profile)
if mut_only == 1:
print "Export only mutant proteins..."
prot_profile = [
prot for prot in prot_profile if prot.mutation != 'REF'
]
records = []
for prot in prot_profile:
records.append(cfunc.protein_to_SeqRecord(prot))
now = strftime("%Y%m%d-%H%M%S", localtime())
out_db_file = output_dir + "mutProteinDB_" + now + ".fa"
SeqIO.write(records, out_db_file, 'fasta')
return
def build_pepDB(refSeq_file, variants_file, output_dir, mut_only, max_miss,
min_len, max_len):
#max_miss = 2
#min_len = 6
#max_len = 144
variants_read = cfunc.read_cmi_var(variants_file)
refSeq_read = cfunc.read_uniprotFa(refSeq_file)
# filter variants to focus on the ones only associated with the longest transcript
refSeq = refSeq_read
# variants = variants_read
# refSeq = cfunc.get_longest_records(refSeq)
variants = {}
for key, var in variants_read.iteritems():
if key in refSeq.keys():
variants[key] = var
# obtain trypsinized peptide profiles considering mutations in R, K, P that affect trypsin digestion
print 'Annotating reference peptides...'
pep_profile = []
len_protein = 0
for key in variants.keys():
eachProtein = refSeq[key]
protein1 = protein(eachProtein['header'], eachProtein['seq'])
protein1.add_trypsin_profile(max_miss=max_miss)
protein1.annotate_pep()
matchVariants = variants[protein1.transcript]
for var in matchVariants:
variant1 = variant(protein1.transcript, var)
variant1.get_seq(refSeq)
if variant1.is_RKP(
): # check whether mutation will affect trypsin digestion
protein1.annotate_pepvar(variant1, max_miss=max_miss)
protein1.exclude_len(min_len=min_len, max_len=max_len)
pep_profile.extend(protein1.trypsin_profile)
len_protein += 1
len_profile = len(pep_profile)
if len_protein % 100 == 0:
print 'Finished %d reference proteins.' % (len_protein)
print 'Annotated %d reference peptides.' % (len_profile)
print '\nFinished %d reference proteins.' % (len_protein)
print 'Annotated %d reference peptides.\n' % (len_profile)
# generate all peptides with single mutations at trypsinized peptide level
print 'Annotating mutant peptides...'
mut_pept = []
len_peptide = 0
for pep in pep_profile:
peptide1 = peptide(pep)
if peptide1.mutation == 'REF': # exclude mutants that affect trypsin digestion
peptide1.find_variants(variants, refSeq)
peptide1.generate_single_mut_peptide()
peptide1.annotate()
peptide1.exclude_len(min_len=min_len, max_len=max_len)
mut_pept.extend(peptide1.annotated_profile)
len_peptide += 1
len_profile = len(mut_pept)
if len_peptide % 10000 == 0:
print 'Finished %d reference peptides.' % (len_peptide)
print 'Annotated %d mutations.' % (len_profile)
print '\nFinished %d reference peptides.' % (len_peptide)
print 'Annotated %d mutations.\n' % (len_profile)
# remove duplicates due to the same nonsense mutation on different miss cleavage yielded peptides
print 'Removing replicates...'
uniqIDs = set()
uniq_mut_pept = []
for pep in mut_pept:
uniqID = '_'.join([pep[0], str(pep[1]),
str(pep[2])
]) #unique peptide defined by seq+position+length
if uniqID not in uniqIDs:
uniq_mut_pept.append(pep)
uniqIDs.update([uniqID])
len_profile = len(uniq_mut_pept)
print 'Removed %d mutant peptides due to nonsense mutation on different miss cleavage yielded peptides.' % (
len(mut_pept) - len_profile)
print 'Annotated %d mutant peptides.' % (len_profile)
pep_profile.extend(uniq_mut_pept)
print 'Finally, annotated %d peptides.' % (len(pep_profile))
if mut_only == 1:
print "Export only mutant peptides..."
pep_profile = [pep for pep in pep_profile if pep[7] != 'REF']
records = []
for pep in pep_profile:
records.append(cfunc.pep_to_SeqRecord(pep))
now = strftime("%Y%m%d-%H%M%S", localtime())
out_db_file = output_dir + "mutPeptideDB_" + now + ".fa"
SeqIO.write(records, out_db_file, 'fasta')
return