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Created by
Dénes Türei
last modified
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# Denes Turei 2019
# turei.denes@gmail.com
import importlib as imp
import os
import re
import csv
import collections
import pypath.homology
import pypath.session_mod
import pypath.ptm
import pypath.mapping
import pypath.progress
FragmentMatch = collections.namedtuple(
'FragmentMatch',
[
'isoform',
'uniprot_offset',
'fragment',
'databases',
'enzymes',
],
)
FragmentMatch.__new__.__defaults__ = (None,) * 2
class SeqLookup(pypath.session_mod.Logger):
"""
Looks up phosphopeptide sequence fragments in UniProt sequences.
Determines the offset of the phosphosites.
"""
reptm = re.compile(
r'(\d+)x'
r'(\w+) '
r'\[([-;\w/]+)\]'
)
reptmsite = re.compile(
r'([A-Z/]+)'
r'(?:([0-9]+))?'
)
mod_types = {
'Phospho': 'phosphorylation',
'Oxidation': 'oxidation',
'Carbamidomethyl': 'carbamidomethylation',
}
def __init__(
self,
seq_fragments_file = None,
ncbi_tax_id = 10090,
output_path = None,
**kwargs
):
self.seq_fragments_file = seq_fragments_file
self.ncbi_tax_id = ncbi_tax_id
self.output_path = output_path
self._set_ptmdb_pickle()
pypath.session_mod.Logger.__init__(self, name = 'seq-lookup')
def reload(self):
modname = self.__class__.__module__
mod = __import__(modname, fromlist = [modname.split('.')[0]])
imp.reload(mod)
new = getattr(mod, self.__class__.__name__)
setattr(self, '__class__', new)
def main(self):
self.load()
self.read()
self.lookup()
self.results_table()
self.export()
self._log('Finished.')
def load(self):
self.load_sequences()
self.load_ptms()
def load_sequences(self):
self._log('Loading sequences for the entire proteome from UniProt.')
self.seq = pypath.homology.SequenceContainer()
self.seq.load_seq(taxon = self.ncbi_tax_id)
def load_ptms(self):
self._log('Loading known PTM sites.')
ptm_args = {
'ncbi_tax_id': self.ncbi_tax_id,
'pickle_file': (
self.ptmdb_pickle
if os.path.exists(self.ptmdb_pickle) else
None
),
}
self.ptmdb = pypath.ptm.PtmAggregator(**ptm_args)
self.save_ptmdb()
def save_ptmdb(self, overwrite = False):
if not os.path.exists(self.ptmdb_pickle) or overwrite:
self.ptmdb.save_to_pickle(pickle_file = self.ptmdb_pickle)
def _set_ptmdb_pickle(self):
self.ptmdb_pickle = os.path.join(
'data',
'ptmdb__%s.pickle' % self.ncbi_tax_id,
)
def read(self):
self._log(
'Reading sequence fragments from `%s`.' % self.seq_fragments_file
)
with open(self.seq_fragments_file, 'r') as fp:
self.seq_frag_raw = list(csv.DictReader(fp))
self.preprocess_fragments()
def preprocess_fragments(self):
PtmRecord = collections.namedtuple(
'PtmRecord',
[
'idx',
'uniprot',
'typ',
'residue',
'offset',
'times',
'data',
],
)
self.fragments = []
prg = pypath.progress.Progress(
len(self.seq_frag_raw),
'Preprocessing sequence fragments',
1,
)
for i, rec in enumerate(self.seq_frag_raw):
prg.step()
all_features = self.reptm.findall(rec['mod'])
for times, typ, mod in all_features:
for mod in mod.split(';'):
residues, offset = self.reptmsite.match(mod).groups()
for residue in residues.split('/'):
for uniprot in pypath.mapping.map_name(
rec['ProtAcc'],
'uniprot',
'uniprot',
ncbi_tax_id = self.ncbi_tax_id,
):
typ = (
self.mod_types[typ]
if typ in self.mod_types else
typ
)
self.fragments.append(
PtmRecord(
idx = i,
uniprot = uniprot,
typ = typ,
residue = residue,
offset = int(offset) if offset else None,
times = times,
data = rec,
)
)
prg.terminate()
def lookup(self):
self._log('Looking up sequence fragments.')
self.lookup_result = []
prg = pypath.progress.Progress(
len(self.fragments),
'Looking up sequence fragments',
1,
)
for frag in self.fragments:
prg.step()
self.lookup_result.extend(self.lookup_frag(frag))
prg.terminate()
def lookup_frag(self, frag):
lookup_result = []
seq = self.seq.get_seq(frag.uniprot, taxon = self.ncbi_tax_id)
if not seq:
self._log(
'Could not find sequence '
'in UniProt: `%s`.' % frag.uniprot
)
return [FragmentMatch(None, None, frag)]
seq_found = False
residue_found = False
for iso, offset in seq.findall(frag.data['peptide_seq']):
seq_found = True
if frag.offset is not None:
uniprot_offsets = (offset + frag.offset,)
else:
uniprot_offsets = [
offset + res_offset
for res_offset in self.substr_find_all(
frag.data['peptide_seq'],
frag.residue,
)
]
for uniprot_offset in uniprot_offsets:
residue_found = True
this_ptm = pypath.intera.Ptm(
protein = frag.uniprot,
isoform = iso,
typ = frag.typ,
residue = pypath.intera.Residue(
identifier = frag.uniprot,
name = frag.residue,
number = uniprot_offset,
)
)
databases, enzymes = (
(
';'.join(sorted(self.ptmdb.ptms[this_ptm].sources)),
';'.join(sorted(self.ptmdb.ptm_to_enzyme[this_ptm])),
)
if this_ptm in self.ptmdb.ptms else
(None, None)
)
lookup_result.append(
FragmentMatch(
isoform = iso,
uniprot_offset = uniprot_offset,
fragment = frag,
databases = databases,
enzymes = enzymes,
)
)
if not seq_found:
self._log(
'Could not find sequence `%s` '
'in any isoform of UniProt `%s`.' % (
frag.data['peptide_seq'],
frag.uniprot,
)
)
lookup_result = [FragmentMatch(None, None, frag)]
elif not residue_found and frag.residue != 'N':
self._log(
'Could not find residue `%s` in '
'sequence fragment `%s` (UniProt: %s).' % (
frag.residue,
frag.data['peptide_seq'],
frag.uniprot,
)
)
lookup_result = [FragmentMatch(None, None, frag)]
return lookup_result
@staticmethod
def substr_find_all(string, sub):
offset = 0
while True:
offset = string.find(sub, offset)
if offset == -1:
break
yield offset
offset += 1
def results_table(self):
ResultRecord = collections.namedtuple(
'ResultRecord',
[
'uniprot',
'isoform',
'residue',
'offset',
'modification',
'times',
'original_id',
'original_uniprot',
'peptide_seq',
'peptide_seq_offset',
'modifications_raw',
'gene',
'p_value',
'q_value',
'diff',
'stat',
'databases',
'enzymes',
]
)
self.result = []
for rec in self.lookup_result:
self.result.append(
ResultRecord(
uniprot = rec.fragment.uniprot,
isoform = rec.isoform,
residue = rec.fragment.residue,
offset = rec.uniprot_offset,
modification = rec.fragment.typ,
times = rec.fragment.times,
original_id = rec.fragment.idx,
original_uniprot = rec.fragment.data['ProtAcc'],
peptide_seq = rec.fragment.data['peptide_seq'],
peptide_seq_offset = rec.fragment.offset,
modifications_raw = rec.fragment.data['mod'],
gene = rec.fragment.data['gene'],
p_value = rec.fragment.data['p-value'],
q_value = rec.fragment.data['q-value'],
diff = rec.fragment.data['diff'],
stat = rec.fragment.data['stat'],
databases = rec.databases,
enzymes = rec.enzymes,
)
)
def export(self):
self.output_path = (
self.output_path or
'%s.uniprot.csv' % self.seq_fragments_file
)
self._log('Exporting results to `%s`.' % self.output_path)
with open(self.output_path, 'w') as fp:
writer = csv.writer(
fp,
delimiter = ',',
quotechar = '"',
quoting = csv.QUOTE_MINIMAL,
)
writer.writerow(self.result[0]._fields)
for row in self.result:
writer.writerow(row)
if __name__ == '__main__':
input_files = [
('data', 'Ursula_D140vsWT_original.csv'),
('data', 'Ursula_E98VvsWT_original.csv'),
]
ncbi_tax_id = 10090
for input_file in input_files:
seq_fragments_file = os.path.join(*input_file)
sl = SeqLookup(
seq_fragments_file = seq_fragments_file,
ncbi_tax_id = ncbi_tax_id,
)
sl.main()
sl._log('Script exiting.')
|
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