def __init__ (self, ref_protein_id, species, ref_exon, alignment_exon):
self.ref_protein_id = ref_protein_id
self.species = species
self.ref_exon = ref_exon
self.alignment_exon = alignment_exon
self.alignment_pieces = process_exon_alignment(self.alignment_exon, self.ref_exon)
self.set_protein_sequences()
self.determine_absolute_coordinates ()
def set_protein_sequences (self):
'''
Loads the alignment pieces and sets their
translations to protein.
'''
pc = ProteinContainer.Instance()
ref_protein = pc.get(self.ref_protein_id)
ref_protein_seq = ref_protein.get_sequence_record().seq
ref_exon_translation = self.ref_exon.sequence[self.ref_exon.frame:].translate()
# remove the stop codon from the last position
if str(ref_exon_translation).endswith("*"):
ref_exon_translation = ref_exon_translation[0:len(ref_exon_translation)-1]
self.alignment_pieces = process_exon_alignment(self.alignment_exon, self.ref_exon)
self.alignment_pieces = set_protein_sequences (self.alignment_pieces)
# find the locations of the exon translation in the protein
exon_start = str(ref_protein_seq).find(str(ref_exon_translation))
exon_stop = exon_start + len(ref_exon_translation)
previous = None
for al_piece in self.alignment_pieces:
if al_piece.type == "coding":
ref_protein_seq_piece = str(al_piece.ref_protein_seq)
if ref_protein_seq_piece.endswith("*"):
ref_protein_seq_piece = ref_protein_seq_piece[0:len(ref_protein_seq_piece)-1]
# make sure that the piece is location within the bounds of the exon translation
for a in list(re.finditer(str(ref_protein_seq_piece), str(ref_protein_seq))):
if a.start() >= exon_start and a.end() <= exon_stop:
al_piece.set_protein_locations (a.start(), a.end())
break
if al_piece.type == "insertion":
al_piece.set_protein_locations(previous.ref_protein_stop, previous.ref_protein_stop + 1)
previous = al_piece
