def __init__(self, residues):
self.residues = residues
self.seq = self.get_peptide_sequence(self.residues)
self.blast_online = BlastSearchOnline()
self.id = ''
self.mapping = {}
self.map_aux()
def __init__(self, residues):
self.residues = residues
self.seq = self.get_peptide_sequence(self.residues)
self.blast_online = BlastSearchOnline()
self.id = ''
self.mapping = {}
self.map_aux()
class AuxProtein(object):
"""
Class storing the mapping of the fusion/auxiliary protein.
"""
residue_list = [
"ARG", "ASP", "GLU", "HIS", "ASN", "GLN", "LYS", "SER", "THR", "HIS",
"HID", "PHE", "LEU", "ILE", "TYR", "TRP", "VAL", "MET", "PRO", "CYS",
"ALA", "GLY"
]
def __init__(self, residues):
self.residues = residues
self.seq = self.get_peptide_sequence(self.residues)
self.blast_online = BlastSearchOnline()
self.id = ''
self.mapping = {}
self.map_aux()
def get_peptide_sequence(self, residues):
"""
Returns a sequence string of a given list of Bio.PDB.Residue objects.
"""
return "".join([
polypeptide.three_to_one(x.resname.replace('HID', 'HIS'))
for x in residues if x.resname in self.residue_list
])
def map_aux(self):
alignments = self.blast_online.run(self.seq)
for alignment in alignments:
self.id = alignment[0]
for hsps in alignment[1].hsps:
self.map_hsps(hsps)
def map_hsps(self, hsps):
"""
Analyzes the High Similarity Protein Segment.
"""
offset = min([int(x.id[1]) for x in self.residues])
q = hsps.query
sbjct = hsps.sbjct
sbjct_counter = hsps.sbjct_start
q_counter = hsps.query_start
for s, q in zip(sbjct, q):
if s == q:
self.mapping[sbjct_counter] = offset - 1 + q_counter
sbjct_counter += 1
q_counter += 1
elif s != '-' and q != '-':
self.mapping[sbjct_counter] = offset - 1 + q_counter
sbjct_counter += 1
q_counter += 1
elif s != '-' and q == '-':
sbjct_counter += 1
else:
sbjct_counter += 1
q_counter += 1
def get_info(self):
return OrderedDict({
"presence": 'YES',
"type": "fusion",
"uniprot": self.id,
"description": "",
"start": min(self.mapping.values()),
"end": max(self.mapping.values()),
"start (pdb)": min(self.mapping.keys()),
"end (pdb)": max(self.mapping.keys()),
})
class AuxProtein(object):
"""
Class storing the mapping of the fusion/auxiliary protein.
"""
residue_list = ["ARG","ASP","GLU","HIS","ASN","GLN","LYS","SER","THR", "HIS", "HID","PHE","LEU","ILE","TYR","TRP","VAL","MET","PRO","CYS","ALA","GLY"]
def __init__(self, residues):
self.residues = residues
self.seq = self.get_peptide_sequence(self.residues)
self.blast_online = BlastSearchOnline()
self.id = ''
self.mapping = {}
self.map_aux()
def get_peptide_sequence(self, residues):
"""
Returns a sequence string of a given list of Bio.PDB.Residue objects.
"""
return "".join([polypeptide.three_to_one(x.resname.replace('HID', 'HIS')) for x in residues if x.resname in self.residue_list])
def map_aux(self):
print('aux1',datetime.now() - startTime)
alignments = self.blast_online.run(self.seq)
print('aux2',datetime.now() - startTime)
for alignment in alignments:
self.id = alignment[0]
for hsps in alignment[1].hsps:
self.map_hsps(hsps)
def map_hsps(self, hsps):
"""
Analyzes the High Similarity Protein Segment.
"""
offset = min([int(x.id[1]) for x in self.residues])
q = hsps.query
sbjct = hsps.sbjct
sbjct_counter = hsps.sbjct_start
q_counter = hsps.query_start
for s, q in zip(sbjct, q):
if s == q:
self.mapping[sbjct_counter] = offset - 1 + q_counter
sbjct_counter += 1
q_counter += 1
elif s != '-' and q != '-':
self.mapping[sbjct_counter] = offset - 1 + q_counter
sbjct_counter += 1
q_counter += 1
elif s != '-' and q == '-':
sbjct_counter += 1
else:
sbjct_counter += 1
q_counter += 1
def get_info(self):
return OrderedDict({
"presence" : 'YES',
"type" : "fusion",
"uniprot" : self.id,
"description" : "",
"start" : min(self.mapping.values()),
"end" : max(self.mapping.values()),
"start (pdb)" : min(self.mapping.keys()),
"end (pdb)" : max(self.mapping.keys()),
})
