def translate_alignment_exons_for_protein(protein_id, exon_number):
'''
Translates all the proteins for which there is SW to gene alignment
'''
algorithm = "sw_gene"
# instantiate all the utilities
logger = Logger.Instance()
dc = DirectoryCrawler()
translation_logger = logger.get_logger("translator")
# instantiate all the containters
eec = EnsemblExonContainer.Instance()
ec = ExonContainer.Instance()
pc = ProteinContainer.Instance()
failed_species = []
assembled_protein_path = dc.get_assembled_protein_path(protein_id)
# for all the species for which it is required to generate translated protein
for species in get_species_list(protein_id, assembled_protein_path):
# get all you need for the processing
assembled_protein_fasta = "%s/%s.fa" % (dc.get_assembled_protein_path(protein_id), species)
exon_key = (protein_id, species, algorithm)
target_prot = pc.get(protein_id)
target_prot_seq = target_prot.get_sequence_record().seq
try:
exons = ec.get(exon_key)
except KeyError:
translation_logger.error("%s,%s,%s" % (protein_id, species, "No exons available"))
failed_species.append(species)
continue
exons_for_transcription = []
# THIS PART WILL NOT EXIST IN THE NEAR FUTURE
last_translated_exon = False
for al_exon in exons.get_ordered_exons():
ref_exon = eec.get(al_exon.ref_exon_id)
trans_exon = Exon_translation(ref_exon, al_exon)
# if we've already bumped into exon with UTR on its end, all the other exons are not viable
if last_translated_exon:
trans_exon.viability = False
if trans_exon.viability:
(trans_exon, last_translated_exon) = chop_off_start_utr(al_exon.ref_exon_id, trans_exon, target_prot_seq, exon_number)
trans_exon = chop_off_end_utr (al_exon.ref_exon_id, trans_exon, target_prot_seq, exon_number, protein_id)
exons_for_transcription.append(trans_exon)
# up to here - this will get trashed
assemble_and_store_protein (protein_id, species, exons_for_transcription, target_prot_seq, assembled_protein_fasta)
create_protein_alignment (protein_id, species)
write_failed_species_to_status(failed_species, assembled_protein_path)
return failed_species
def set_frames_to_coding_exons_batch(protein_list):
exon_container = ExonContainer.Instance()
for protein_id in protein_list:
for species in get_species_list(protein_id, None):
try:
exons = exon_container.get((protein_id, species, "ensembl"))
exons.set_coding_exon_frames()
except Exception:
pass
def create_msa_alignments ():
dc = DirectoryCrawler()
pc = ProteinContainer.Instance()
dmc = DataMapContainer.Instance()
acg = AlignmentCommandGenerator()
fill_all_containers(False)
for (prot_id, exon_num) in get_protein_list():
if not check_status_file(prot_id):
continue
ref_prot_rec = pc.get(prot_id).get_sequence_record()
exoloc_proteins = []
ensembl_proteins = []
exoloc_proteins.append(ref_prot_rec)
ensembl_proteins.append(ref_prot_rec)
assembled_dir = dc.get_assembled_protein_path(prot_id)
for fasta in sorted(os.listdir(assembled_dir)):
if fasta == "Homo_sapiens.fa":
continue
abs_fasta = "%s/%s" % (assembled_dir, fasta)
prot_rec = load_fasta_single_record(abs_fasta, IUPAC.protein)
exoloc_proteins.append(prot_rec)
species_list = get_species_list(prot_id, None)
for species in species_list:
if species == "Homo_sapiens":
continue
data_map = dmc.get((prot_id, species))
prot_rec = pc.get(data_map.protein_id).get_sequence_record()
prot_rec.id = species
ensembl_proteins.append(prot_rec)
msa_exoloc_path = "%s/msa_exoloc.fa" % dc.get_mafft_path(prot_id)
msa_ensembl_path = "%s/msa_ensembl.fa" % dc.get_mafft_path(prot_id)
write_seq_records_to_file(msa_exoloc_path, exoloc_proteins)
write_seq_records_to_file(msa_ensembl_path, ensembl_proteins)
cmd = acg.generate_mafft_command(msa_exoloc_path, "%s/msa_exoloc.afa" % dc.get_mafft_path(prot_id))
print cmd
os.system(cmd)
cmd = acg.generate_mafft_command(msa_ensembl_path, "%s/msa_ensembl.afa" % dc.get_mafft_path(prot_id))
print cmd
os.system(cmd)
def create_species_msa_alignments ():
dc = DirectoryCrawler()
pc = ProteinContainer.Instance()
dmc = DataMapContainer.Instance()
acg = AlignmentCommandGenerator()
fill_all_containers(False)
for (prot_id, exon_num) in get_protein_list():
if not check_status_file(prot_id):
continue
ref_prot_rec = pc.get(prot_id).get_sequence_record()
ref_prot_rec.id = "Homo_sapiens"
assembled_dir = dc.get_assembled_protein_path(prot_id)
species_list = get_species_list(prot_id, None)
for species in species_list:
protein_recs = []
protein_recs.append(ref_prot_rec)
if species == "Homo_sapiens":
continue
data_map = dmc.get((prot_id, species))
prot_rec = pc.get(data_map.protein_id).get_sequence_record()
prot_rec.id = species
protein_recs.append(prot_rec)
if "%s.fa" % species in os.listdir(assembled_dir):
exoloc_protein_rec = load_fasta_single_record("%s/%s.fa" % (assembled_dir, species), IUPAC.protein)
protein_recs.append(exoloc_protein_rec)
msa_species_path = "%s/%s.fa" % (dc.get_mafft_path(prot_id), species)
if len(protein_recs) == 1:
continue
write_seq_records_to_file(msa_species_path, protein_recs)
cmd = acg.generate_mafft_command(msa_species_path, "%s/%s.afa" % (dc.get_mafft_path(prot_id), species))
print cmd
os.system(cmd)
os.remove(msa_species_path)
def get_SW_exon_targets(self, protein_id):
'''
@param protein_id: retrieves the list of species not aligned with SW_exon for that protein
'''
path = self.crawler.get_SW_exon_path(protein_id)
return get_species_list(protein_id, path)
def main ():
#ERROR FILE:::
err_f = open('/home/marioot/err_status_monday.txt', 'w')
fill_all_containers(True)
protein_tuples = get_protein_list()
ec = ExonContainer.Instance()
beac = BestExonAlignmentContainer.Instance()
dc = DirectoryCrawler()
for (protein_id, exon_num) in protein_tuples:
if int(exon_num) > 15:
print "too big"
continue
species_list = get_species_list(protein_id, None)
try:
ref_exons = ec.get((protein_id, "Homo_sapiens", "ensembl"))
except KeyError:
print "ERROR: No protein %s" % protein_id
continue
for species in species_list:
try:
print "\nBest_exon_al: %s, %s" % (protein_id, species)
err_f.write("%s, %s" % (protein_id, species))
bpp = BestProteinProduct (protein_id, species, "Homo_sapiens")
bpp.load_alignments()
bpp.decide_on_best_exons()
#bpp.patch_interexon_AAS()
for ref_exon in ref_exons.get_coding_exons():
best_exon_alignment = bpp.best_exons[ref_exon.exon_id]
if best_exon_alignment:
beac.add(ref_exon.exon_id, species, best_exon_alignment)
print "%d. Exon status: %s (%s)" % (ref_exon.ordinal, best_exon_alignment.status, ref_exon.exon_id)
if best_exon_alignment.sw_gene_alignment:
print ref_exon.sequence[ref_exon.frame:].translate()
best_exon_alignment.sw_gene_alignment.create_cDNA()
print "\tAdded %2d alignment pieces" % (len(best_exon_alignment.sw_gene_alignment.alignment_pieces))
for al_piece in best_exon_alignment.sw_gene_alignment.alignment_pieces:
print "\t\t%s:" % (al_piece.type),
if al_piece.type in ["coding", "insertion"]:
print "PROT: %d-%d, GENOME: %d-%d, %s" % (al_piece.ref_protein_start,
al_piece.ref_protein_stop,
al_piece.genomic_start,
al_piece.genomic_stop,
al_piece.sequence_id)
print "\t\t\tHUMAN:", al_piece.ref_protein_seq
print "\t\t\tSPEC :", al_piece.spec_protein_seq
else:
print
whole_prot = bpp.get_spec_protein_translation()
whole_prot_rec = SeqRecord(whole_prot, id = species, description = "assembled_protein")
file_name = "%s/%s.fa" % (dc.get_assembled_protein_path(protein_id), species)
SeqIO.write(whole_prot_rec, file_name, "fasta")
print beac.get("ENSE00002199725", species)
except Exception, e:
print '{0} {1} \n'.format(protein_id, species)
err_f.write('{0} {1} \n'.format(protein_id, species))
