def build_db(self):
"""TODO(nh2tran): docstring."""
print("".join(["="] * 80)) # section-separating line
print("WorkerDB.build_db()")
# parse the input fasta file into a list of sequences
# more about SeqIO and SeqRecord: http://biopython.org/wiki/SeqRecord
with open(self.db_fasta_file, "r") as handle:
record_iterator = SeqIO.parse(handle, "fasta")
record_list = list(record_iterator)
sequence_list = [str(record.seq) for record in record_list]
print("Number of protein sequences: {0:d}".format(
len(sequence_list)))
# cleave protein sequences into a list of unique peptides
# more about pyteomics.parser.cleave and cleavage rules:
# https://pythonhosted.org/pyteomics/api/parser.html
peptide_set = set()
for sequence in sequence_list:
peptide_set.update(
(parser.cleave(sequence=sequence,
rule=parser.expasy_rules[self.cleavage_rule],
missed_cleavages=self.num_missed_cleavage)))
peptide_list = list(peptide_set)
# skip peptides with undetermined amino acid 'X', or 'B'
peptide_list = [
list(peptide) for peptide in peptide_list
if not ('X' in peptide or 'B' in peptide)
]
peptide_count = len(peptide_list)
print("Number of peptides: {0:d}".format(peptide_count))
# replace "L" by "I"
for index, peptide in enumerate(peptide_list):
peptide = ['I' if x == 'L' else x for x in peptide]
peptide_list[index] = peptide
# update fixed modifications
for index, peptide in enumerate(peptide_list):
peptide = [
x + 'mod' if x in self.fixed_mod_list else x for x in peptide
]
peptide_list[index] = peptide
# for each peptide, find the mass and the max modification mass
peptide_mass_array = np.zeros(peptide_count)
pepmod_maxmass_array = np.zeros(peptide_count)
for index, peptide in enumerate(peptide_list):
peptide_mass_array[index] = self._compute_peptide_mass(peptide)
pepmod = [
x + 'mod' if x in self.var_mod_list else x for x in peptide
]
pepmod_maxmass_array[index] = self._compute_peptide_mass(pepmod)
self.peptide_count = peptide_count
self.peptide_list = peptide_list
self.peptide_mass_array = peptide_mass_array
self.pepmod_maxmass_array = pepmod_maxmass_array
def cleave_peptide(db,inp):
dict_of_sequences={}
for i in SeqIO.parse(open(db), "fasta"):
sequence = str(i.seq)
peptides = parser.cleave(sequence,parser.expasy_rules['trypsin'])
size = [j for j in peptides if (len(j)>6 and len(j)<=35)]
dict_of_sequences[i.id.split("|")[1]]=len(size)
summed = {}
for j1 in open(inp):
if not j1.startswith("Sequence"):
peptide, accession, intensity = j1.strip().split("\t")
for k in accession.split(";"):
if k in summed:
summed[k] += float(intensity)
else:
summed[k]=0
summed[k] += float(intensity)
for each in summed:
lengths = dict_of_sequences.get(each,0)
if lengths==0:
ibaq=0
else:
ibaq = float(summed[each])/lengths
try:
print "\t".join([str(each), str(ibaq),str(math.log10(ibaq))])
except:
print "\t".join([str(each), str(ibaq),"0"])
def build_db(self):
"""TODO(nh2tran): docstring."""
print("".join(["="] * 80)) # section-separating line
print("WorkerDB: build_db()")
# parse the input fasta file into a list of sequences
# more about SeqIO and SeqRecord: http://biopython.org/wiki/SeqRecord
with open(self.db_fasta_file, "r") as handle:
record_iterator = SeqIO.parse(handle, "fasta")
record_list = list(record_iterator)
print("Number of protein sequences: {0:d}".format(len(record_list)))
# cleave protein sequences into a list of unique peptides
# more about pyteomics.parser.cleave and cleavage rules:
# https://pythonhosted.org/pyteomics/api/parser.html
# create a peptide to protein accession id map.
peptide_2_protein_id = {}
for record in record_list:
protein_sequence = str(record.seq)
protein_id = str(record.id)
cleaved_peptide_set = parser.cleave(
sequence=protein_sequence,
rule=parser.expasy_rules[self.cleavage_rule],
missed_cleavages=self.num_missed_cleavage)
for peptide in cleaved_peptide_set:
if any(x in peptide for x in ['X', 'B', 'U', 'Z']):
# skip peptides with undetermined amino acid ['X', 'B', 'U', 'Z']
continue
if peptide not in peptide_2_protein_id:
peptide_2_protein_id[peptide] = {protein_id}
else:
peptide_2_protein_id[peptide].add(protein_id)
peptide_list = [list(peptide) for peptide in peptide_2_protein_id.keys()]
peptide_list = [[x + 'mod' if x in self.fixed_mod_list else x for x in peptide] for peptide in peptide_list ]
peptide_count = len(peptide_list)
print("Number of peptides: {0:d}".format(peptide_count))
# for each peptide, find the mass and the max modification mass
peptide_mass_array = np.zeros(peptide_count)
pepmod_maxmass_array = np.zeros(peptide_count)
for index, peptide in enumerate(peptide_list):
peptide_mass_array[index] = self._compute_peptide_mass(peptide)
pepmod = [x + 'mod' if x in self.var_mod_list else x for x in peptide]
pepmod_maxmass_array[index] = self._compute_peptide_mass(pepmod)
self.peptide_count = peptide_count
self.peptide_list = peptide_list
self.peptide_mass_array = peptide_mass_array
self.pepmod_maxmass_array = pepmod_maxmass_array
self.peptide_2_protein_id = peptide_2_protein_id
def print_target_decoy_composition(self):
"""
Print the number of target peptides vs decoy peptides in a Fasta database
:return:
"""
target_aa_composition = {i: 0 for i in [aa for aa in PYGPATK_ALPHABET]}
decoy_aa_composition = {i: 0 for i in [aa for aa in PYGPATK_ALPHABET]}
target_sequence = ''
decoy_sequence = ''
fasta = SeqIO.parse(self._output_file, 'fasta')
target_peptides = {}
decoy_peptides = {}
pep_count_in_both = 0
for record in fasta:
peptides = cleave(
sequence=str(record.seq),
rule=PYGPATK_ENZYMES.enzymes[self._enzyme]['cleavage rule'],
missed_cleavages=self._max_missed_cleavages,
min_length=self._min_peptide_length)
if self._decoy_prefix in record.id:
decoy_sequence = decoy_sequence + str(record.seq)
else:
target_sequence = target_sequence + str(record.seq)
for peptide in peptides:
if self._decoy_prefix in record.id:
decoy_peptides[peptide] = 'decoy'
if peptide in target_peptides:
target_peptides.pop(peptide)
pep_count_in_both += 1
else:
if peptide not in decoy_peptides:
target_peptides[peptide] = 'target'
print('Number of target peptides: {} and Decoy Peptides: {}'.format(
len(target_peptides), len(decoy_peptides)))
target_percentage = (
len(target_peptides) /
(len(target_peptides) + len(decoy_peptides))) * 100
print('% Target peptides {:.1f}'.format(target_percentage))
decoy_percentage = (len(decoy_peptides) /
(len(target_peptides) + len(decoy_peptides))) * 100
print('% Decoy peptides {:.1f}'.format(decoy_percentage))
duplicate_percentage = (
pep_count_in_both /
(len(target_peptides) + len(decoy_peptides))) * 100
print('Number of peptides in Target and Decoy {}, Percentage {:.1f}'.
format(pep_count_in_both, duplicate_percentage))
target_aa_composition = self.count_aa_in_dictionary(
target_aa_composition, target_sequence)
decoy_aa_composition = self.count_aa_in_dictionary(
decoy_aa_composition, decoy_sequence)
self.print_aa_composition_rate(target_aa_composition,
decoy_aa_composition)
def digetsProteinFromFASTA():
sequenceIter = fasta.read(source=options.fasta)
uniquePeptides = set()
for s in sequenceIter:
newPeptides = parser.cleave(s.sequence,
'trypsin',
missed_cleavages=options.missed,
min_length=options.minLength)
uniquePeptides.update(newPeptides)
uniquePeptides = list(uniquePeptides)
return [Peptide(x) for x in uniquePeptides]
def digest(prot):
# print(prot)
dtype = [('seq', np.unicode_, MAX_LENGTH_OF_PEP), ('pcMass', float)]
pepsWithMass = np.array([], dtype)
peps = list(
parser.cleave(prot,
parser.expasy_rules["trypsin"],
missed_cleavages=MISSED_CLEAVAGES,
min_length=MIN_LENGTH_OF_PEP))
# if 'MESYHKPDQQK' in peps:
# print(peps)
# if len(peps) != 0:
# firstPep = peps[0]
# if firstPep == 'MESYHKPDQQK':
# print(firstPep)
# nTermPep = firstPep[0].lower() + firstPep[1:]
# peps.append(nTermPep)
nTermPeps = []
oxMPeps = []
for pep in peps:
# print(pep)
# a = prot.index(pep)
# if pep not in prot:
# print(pep)
if prot.index(pep) == 0:
nTermPep = pep[0].lower() + pep[1:]
nTermPeps.append(nTermPep)
elif 'M' in pep:
indexs = [M.start() for M in re.finditer('M', pep)]
for i in indexs:
oxMPep = pep[0:i] + 'm' + pep[i + 1:]
oxMPeps.append(oxMPep)
peps.extend(nTermPeps)
peps.extend(oxMPeps)
peps = [
pep for pep in peps
if (len(pep) <= MAX_LENGTH_OF_PEP and 'B' not in pep and 'J' not in pep
and 'X' not in pep and 'Z' not in pep and 'O' not in pep
and 'U' not in pep)
]
pepsWithMass = np.array([tuple([pep, calcuSeqMass(pep)]) for pep in peps],
dtype)
return pepsWithMass
def test_cleave_semi(self):
self.assertEqual(
parser._cleave('PEPTIDEKS',
parser.expasy_rules['trypsin'],
semi=True),
[
'PEPTIDEK', 'P', 'PE', 'PEP', 'PEPT', 'PEPTI', 'PEPTID',
'EPTIDEK', 'PTIDEK', 'TIDEK', 'IDEK', 'DEK', 'EK', 'K', 'S'
])
self.assertEqual(
parser.cleave('PEPTIDEKS',
parser.expasy_rules['trypsin'],
semi=True),
{
'PEPTIDEK', 'P', 'PE', 'PEP', 'PEPT', 'PEPTI', 'PEPTID',
'EPTIDEK', 'PTIDEK', 'TIDEK', 'IDEK', 'DEK', 'EK', 'K', 'S'
})
def digest(prot):
peps = list(
parser.cleave(prot,
parser.expasy_rules["trypsin"],
missed_cleavages=MISSED_CLEAVAGES,
min_length=MIN_LENGTH_OF_PEP))
peps = [
pep for pep in peps
if (len(pep) <= MAX_LENGTH_OF_PEP and 'B' not in pep and 'J' not in pep
and 'X' not in pep and 'Z' not in pep and 'O' not in pep
and 'U' not in pep)
]
dropMPeps = []
variableModPeps = []
anyNtermQGlu2PyrogluPeps = []
protNtermAcetylPeps = []
# m Drop M
for pep in peps:
if pep[0] == 'M' and prot.find(pep) == 0:
dropMPeps.append(pep[1:])
peps.extend(dropMPeps)
# prot nTerm Acetyl
for pep in peps:
if prot.find(pep) == 0:
protNtermAcetylPeps.append('5' + pep)
for pep in dropMPeps:
protNtermAcetylPeps.append('5' + pep)
# peps.extend(protNtermAcetylPeps)
# pep nterm Q to pyro Q acid
for pep in peps:
if pep[0] == 'Q' and prot.find(pep) != 0:
anyNtermQGlu2PyrogluPeps.append('q' + pep[1:])
peps.extend(anyNtermQGlu2PyrogluPeps)
# variable mod M oxidi.
for pep in peps:
variableModPeps.extend(getVariableModPeps('M', 'm', pep))
peps.extend(variableModPeps)
return peps
def digest_proteins(fasta_file):
protein_df = pd.DataFrame() # Initialize a dataframe to store results
counter = 0
for protein in tqdm(SeqIO.parse(fasta_file, "fasta")):
protein_sequence = str(protein.seq).upper()
# cleave initial "start" methionine if present
if protein_sequence[0] == "M":
protein_sequence = protein_sequence[1:]
# digest proteins into peptides following Arg-C cleavage (r'R')
# glu-c == r'[DE]'
# peptides = list(parser.cleave(protein_sequence, parser.expasy_rules['arg-c']))
peptides = list(parser.cleave(protein_sequence, '[DE]'))
# get the aa residue positions for the peptides to later link residue PTM positions to the peptide
initial_index = []
terminal_index = []
for pep in peptides:
initial_aa_pos = 1 + int(protein_sequence.index(
pep)) # +1 for zero-based array indexing
terminal_aa_pos = initial_aa_pos + len(pep)
initial_index.append(initial_aa_pos)
terminal_index.append(terminal_aa_pos)
# add this protein to the dataframe
new_df = pd.DataFrame({
'protein': [protein.id] * len(peptides),
'peptide_sequence': peptides,
'initial_aa_index': initial_index,
'terminal_aa_index': terminal_index
})
protein_df = protein_df.append(new_df)
protein_df = protein_df[
protein_df['peptide_sequence'].notna()] # drop any nan peptides(?)
protein_df = protein_df[protein_df['peptide_sequence'].str.len() >=
4] # drop peptides <4 aa
protein_df = protein_df[protein_df['peptide_sequence'].str.len() <=
40] # drop peptides >40 aa
sys.stdout.write("Finished in silico digestion and generating peptides.\n")
return (protein_df)
def read_fasta_sequences(fasta_file):
""" Read sequence records from a FASTA file. """
sequence_records = []
for description, sequence in fasta.read(fasta_file):
# Initialize sequence record with sequence string.
sequence_record = {'sequence': sequence}
# Get sequence info.
description_parts = description.split()
sequence_record['id'] = description_parts[0]
# Get the sequence's peptides.
sequence_record['peptides'] = parser.cleave(
sequence,
parser.expasy_rules['trypsin'],
missed_cleavages=1 #max no. of missed cleavages.
)
# Save the sequence record, keyed by the id.
sequence_records.append(sequence_record)
return sequence_records
def prot_to_peprec(protein):
params = get_params()
tmp = pd.DataFrame(
columns=['spec_id', 'peptide', 'modifications', 'charge'])
pep_count = 0
for peptide in cleave(str(protein.seq), expasy_rules['trypsin'],
params['missed_cleavages']):
if False not in [
aa not in peptide for aa in ['B', 'J', 'O', 'U', 'X', 'Z']
]:
if params['min_peplen'] <= len(peptide) < int(
params['max_pepmass'] / 186 + 2):
if not mass.calculate_mass(
sequence=peptide) > params['max_pepmass']:
pep_count += 1
row = {
'spec_id': '{}_{:03d}'.format(protein.id, pep_count),
'peptide': peptide,
'modifications': '-',
'charge': np.nan
}
tmp = tmp.append(row, ignore_index=True)
return tmp
geneError += 1
gError.append(identifier)
match4 = re.search(r'\\PE=(.+?) \\', record.description)
if match4:
pe = match4.group(1)
else:
pe = ''
print(f'WARNING: Unable to find PE value in {record.description}')
match5 = re.search(r'\((.{0,5})\|(.{0,5})\|PEFF:\d+\|mature protein\)',
record.description)
x = len(
re.findall(r'\((.{0,5})\|(.{0,5})\|PEFF:\d+\|mature protein\)',
record.description))
if x > 1:
mature = fixed_sequence
peptides = parser.cleave(mature, 'trypsin')
for peptide in peptides:
if 9 <= len(peptide) <= 40:
trypnum += 1
if match5:
if match5.group(1) == '?' or match5.group(2) == '?':
matureUnknown += 1
mUnknown.append(identifier)
mature = fixed_sequence
peptides = parser.cleave(mature, 'trypsin')
for peptide in peptides:
if 9 <= len(peptide) <= 40:
trypnum += 1
else:
start = int(match5.group(1))
end = int(match5.group(2))
"""
Created on Fri Mar 22 11:28:43 2013
@author: ilya
"""
from pyteomics import fasta, mgf, parser
import pylab
fasta_file = '/home/ilya/src/pyteomics/RhoEcoli.fasta'
mgf_file = '/home/ilya/src/pyteomics/MultiConsensus.mgf'
peptides = set()
with open(fasta_file) as fi:
for description, sequence in fasta.read(fi):
new_peptides = parser.cleave(sequence, parser.expasy_rules['trypsin'])
peptides.update(new_peptides)
print "UNIQUE PEPTIDES"
print peptides
with open(mgf_file) as fi:
for spectrum in mgf.read(fi):
pylab.figure()
pylab.xlabel('m/z, Th')
pylab.ylabel('Intensity, rel.units')
pylab.bar(spectrum['m/z array'], spectrum['intensity array'], width=0.1, linewidth=2, edgecolor='black')
pylab.show()
inp = raw_input("Show more?")
if inp != "yes":
break;
def pypgatk_decoy_database(self):
"""
Create a decoy database from a proteomics database
target db is digested and only digested peptides > _peptide_length are kept
next, each target protein is reversed and digested, all peptides are kept
regardless of their length.
The list of digested peptides from the reversed protein are iterated:
- small peptides are kept (len < _peptide_length)
- peptides not found in target are kep
- peptides with a match are shuffled for max_iterations, if a non-target
peptide was found then written otherwise the peptide is skipped unless
the _keep_target_hits option is true.
:return:
"""
# Create empty sets to add all target and decoy peptides
upeps = set()
noAlternative = set()
# Open FASTA file using first cmd line argument
fasta = SeqIO.parse(self._input_fasta, 'fasta')
# loop each seq in the file
for record in fasta:
seq = str(record.seq)
if not self._isobaric:
seq = seq.replace('I', 'L')
# digest sequence add peptides to the target set
upeps.update(
cleave(sequence=seq,
rule=PYGPATK_ENZYMES.enzymes[self._enzyme]
['cleavage rule'],
missed_cleavages=self._max_missed_cleavages,
min_length=self._min_peptide_length))
# open orary decoy FASTA file
with open(self._output_file, 'w') as outfa:
fasta = SeqIO.parse(self._input_fasta, 'fasta')
targets = []
decoys = []
for i, record in enumerate(fasta):
protseq = str(record.seq)
targets.append(protseq)
revprotseq = []
# output target protein
seq = str(record.seq)
id_protein = record.id
description = record.description
outfa.write('>' + id_protein + ' ' + description + '\n')
outfa.write(seq + '\n')
for seq in protseq.split('*'):
if not seq:
continue
if not self._isobaric:
seq = seq.replace('I', 'L')
# reverse and switch protein sequence
decoyseq = self.revswitch(
seq, self._no_switch, PYGPATK_ENZYMES.enzymes[
self._enzyme]['cleavage sites'])
decoy_peps = cleave(sequence=decoyseq,
rule=PYGPATK_ENZYMES.enzymes[
self._enzyme]['cleavage rule'],
missed_cleavages=0,
min_length=0)
# if any of the digested peptides are found in the targets (upeps) then shuffle
checked_decoy_peps = []
for decoy_pep in decoy_peps:
if len(decoy_pep) < self._min_peptide_length:
checked_decoy_peps.append(decoy_pep)
continue
found_in_target = False
aPep = ''
if decoy_pep in upeps:
found_in_target = True
else:
checked_decoy_peps.append(decoy_pep)
continue
if found_in_target and not self._no_suffle and decoy_pep not in noAlternative:
aPep = decoy_pep
# shuffle until aPep is not in target set (maximum of 10 iterations)
i = 0
while aPep in upeps and i < self._max_iterations:
# increment iteration counter
i += 1
# shuffle peptide
aPep = self.shuffle(aPep)
# check if shuffling has an effect if not end iterations
if aPep == decoy_pep:
i = self._max_iterations
# warn if peptide has no suitable alternative, add to removal list
if i == self._max_iterations:
noAlternative.add(decoy_pep)
aPep = ''
# if decoy is generated then add to the list of peptides
if aPep:
checked_decoy_peps.append(aPep)
else:
if self._keep_target_hits:
checked_decoy_peps.append(decoy_pep)
# finally join the peptides to generate protein decoy
if checked_decoy_peps:
revprotseq.append(''.join(checked_decoy_peps))
outfa.write('>{}\n{}\n'.format(
self._decoy_prefix + str(record.id) + ' ' +
record.description, '*'.join(revprotseq)))
decoys.append('*'.join(revprotseq))
with open(
self._output_file.replace('.fa', '') + '_noAlternative.fa',
'w') as noAlternative_outfa:
noAlternative_outfa.write('\n'.join(noAlternative) + '\n')
print(
'Number of skipped tryptic peptides in decoy db (no alternatives): {}'
.format(len(noAlternative)))
print(
'Total number of amino acids in target and decoy databases: ',
len(''.join(targets)), len(''.join(decoys)))
def generate_decoypyrat_database(self):
"""
Create a decoy database from a proteomics database this method is presented in manuscript:
J Proteomics Bioinform. 2016 Jun 27; 9(6): 176–180. PMCID: PMC4941923
DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics
:return:
"""
# Create empty sets to add all target and decoy peptides
upeps = set()
dpeps = set()
# Counter for number of decoy sequences
dcount = 0
# Open FASTA file using first cmd line argument
# fasta = SeqIO.parse(self._input_fasta, 'fasta')
with open(self._input_fasta) as handle:
# open temporary decoy FASTA file
with open(self._temp_file, 'w') as outfa:
# loop each seq in the file
for value in SimpleFastaParser(handle):
seq = value[1]
description = value[0]
dcount += 1
# make sequence isobaric (check args for switch off)
if not self._isobaric:
seq = seq.replace('I', 'L')
# digest sequence add peptides to set
upeps.update(
cleave(sequence=seq,
rule=PYGPATK_ENZYMES.enzymes[self._enzyme]
['cleavage rule'],
missed_cleavages=0,
min_length=self._min_peptide_length))
# reverse and switch protein sequence
decoyseq = self.revswitch(
seq, self._no_switch, PYGPATK_ENZYMES.enzymes[
self._enzyme]['cleavage sites'])
# do not store decoy peptide set in reduced memory mode
if not self._memory_save:
# update decoy peptide set
dpeps.update(
cleave(sequence=decoyseq,
rule=PYGPATK_ENZYMES.enzymes[self._enzyme]
['cleavage rule'],
missed_cleavages=0,
min_length=self._min_peptide_length))
# write decoy protein accession and sequence to file
outfa.write('>' + self._decoy_prefix + description + '\n')
outfa.write(decoyseq + '\n')
# Summarise the numbers of target and decoy peptides and their intersection
nonDecoys = set()
print("proteins:" + str(dcount))
print("target peptides:" + str(len(upeps)))
# Reloop decoy file in reduced memory mode to store only intersecting decoys
if self._memory_save:
# open temp decoys
with open(self._temp_file, "rt") as fin:
for line in fin:
# if line is not accession
if line[0] != '>':
# digest protein
for p in cleave(sequence=line.rstrip(),
rule=PYGPATK_ENZYMES.enzymes[
self._enzyme]['cleavage rule'],
missed_cleavages=0,
min_length=self._min_peptide_length):
# check if in target peptides if true then add to nonDecoys
if p in upeps:
nonDecoys.add(p)
fin.close()
print("decoy peptides: !Memory Saving Made!")
else:
# can only report total number in normal memory mode
print("decoy peptides:" + str(len(dpeps)))
# find intersecting peptides
nonDecoys = upeps.intersection(dpeps)
print("#intersection:" + str(len(nonDecoys)))
# if there are decoy peptides that are in the target peptide set
if len(nonDecoys) > 0 and self._no_suffle == False:
# create empty dictionary with bad decoys as keys
dAlternative = dict.fromkeys(nonDecoys, '')
noAlternative = list()
# loop bad decoys / dictionary keys
for dPep in dAlternative:
i = 0
aPep = dPep
# shuffle until aPep is not in target set (maximum of 10 iterations)
while aPep in upeps and i < self._max_iterations:
# increment iteration counter
i += 1
# shuffle peptide
aPep = self.shuffle(dPep)
# check if shuffling has an effect if not end iterations
if aPep == dPep:
i = self._max_iterations
# update dictionary with alternative shuffled peptide
dAlternative[dPep] = aPep
# warn if peptide has no suitable alternative, add to removal list
if i == self._max_iterations:
noAlternative.append(dPep)
print(str(len(noAlternative)) + ' have no alternative peptide')
# remove peptides with no alternative
for p in noAlternative:
del dAlternative[p]
# Free up memory by clearing large sets of peptides
upeps.clear()
dpeps.clear()
# open second decoy file
with open(self._output_file, "wt") as fout:
# Attach the target sequences to the database
# fasta = SeqIO.parse(self._input_fasta, 'fasta')
with open(self._input_fasta) as handle:
for value in SimpleFastaParser(handle):
description = value[0]
seq = value[1]
fout.write('>' + description + '\n')
fout.write(seq + '\n')
# open original decoy file
with open(self._temp_file, "rt") as fin:
# loop each line of original decoy fasta
for line in fin:
# if line is not accession replace peptides in dictionary with alternatives
if line[0] != '>':
# digest decoy sequence
for p in cleave(
sequence=line.rstrip(),
rule=PYGPATK_ENZYMES.enzymes[
self._enzyme]['cleavage rule'],
missed_cleavages=0,
min_length=self._min_peptide_length):
# store decoy peptide for final count
dpeps.add(p)
# if decoy peptide is in dictionary replace with alternative
if p in dAlternative:
line = line.replace(p, dAlternative[p])
fout.write(line)
fin.close()
fout.close()
# delete temporary file
os.remove(self._temp_file)
else:
os.rename(self._temp_file, self._output_file)
print("final decoy peptides:" + str(len(dpeps)))
def digest(prot):
# print(prot)
peps = list(parser.cleave(prot, parser.expasy_rules["trypsin"], missed_cleavages = 0, min_length = MIN_LENGTH_OF_PEP))
peps = [pep for pep in peps if len(pep) <= MAX_LENGTH_OF_PEP]
return peps
arg_parser.add_argument('-v', '--verbosity', action='count',
help='increase output verbosity')
args = arg_parser.parse_args()
# TODO: Do it proper way - using os.path
out_file = args.fasta_file + '.peptides'
peptides = []
with fasta.read(args.fasta_file) as reader, open(out_file,'w') as writer:
# Build a set of peptides for each fasta sequence
if args.verbosity >= 1:
print 'Building digests...'
for description, sequence in reader:
peps = parser.cleave(sequence, parser.expasy_rules[args.enz], args.missed)
peps = [x for x in peps if len(x) > args.min]
writer.write('Peptides for {seq} ({enz} cleavage)\n'.format(
seq=description, enz=args.enz))
writer.write('...\t{n} missed cleavages\n'.format(n=args.missed))
writer.write('\n'.join(peps)+'\n')
peptides.append(set(peps))
if args.verbosity >= 2:
print '...\t{n} peptides for {prot}'.format(n=len(peps),prot=description)
# Identify unique peptides for each fasta sequence
if args.verbosity >= 1:
print 'Finding unique peptides...'
for peps in peptides:
rest = [x for x in peptides if x is not peps]
unique = peps - set().union(*rest)
def digest_protein(protein=None):
digest = parser.cleave(protein, '[KR]', missed_cleavages=3, min_length=6)
return digest
def trypsin(aa):
return parser.cleave(aa,
parser.expasy_rules['trypsin'],
min_length=7,
missed_cleavages=1)