def create_protein_alignment(protein_id, species):
'''
Generates the SW alignment of three protein sequences:
reference species protein, the assembled protein and the ensembl species protein
@param protein_id: referent protein id
@param species: species (latin)
'''
sequences_for_fasta = []
dc = DirectoryCrawler()
pc = ProteinContainer.Instance()
dmc = DataMapContainer.Instance()
acg = AlignmentCommandGenerator()
tpc = TranslatedProteinContainer.Instance()
data_map = dmc.get((protein_id, species))
# get all the proteins
ref_protein = pc.get(protein_id)
species_protein = pc.get(data_map.protein_id)
assembled_protein = tpc.get(protein_id, species)
sequences_for_fasta.append(ref_protein.get_sequence_record())
sequences_for_fasta.append(assembled_protein.get_sequence_record())
sequences_for_fasta.append(species_protein.get_sequence_record())
msa_fasta = "%s/%s.fa" % (dc.get_mafft_path(protein_id), species)
msa_afa = "%s/%s.afa" % (dc.get_mafft_path(protein_id), species)
msa_fasta_file = open(msa_fasta, "w")
SeqIO.write(sequences_for_fasta, msa_fasta_file, "fasta")
msa_fasta_file.close()
mafft_cmd = acg.generate_mafft_command(msa_fasta, msa_afa)
os.system(mafft_cmd)
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)
