def multiple_exon_alnmt(gene_list, db_info):
print "process pid: %d, length of gene list: %d" % ( get_process_id(), len(gene_list))
[local_db, ensembl_db_name] = db_info
db = connect_to_mysql()
cfg = ConfigurationReader()
acg = AlignmentCommandGenerator()
cursor = db.cursor()
# find db ids adn common names for each species db
[all_species, ensembl_db_name] = get_species (cursor)
species = 'homo_sapiens'
switch_to_db (cursor, ensembl_db_name[species])
gene_ids = get_gene_ids (cursor, biotype='protein_coding', is_known=1)
# for each human gene
gene_ct = 0
tot = 0
ok = 0
no_maps = 0
no_pepseq = 0
no_orthologues = 0
min_similarity = cfg.get_value('min_accptbl_exon_sim')
#gene_list.reverse()
for gene_id in gene_list:
start = time()
gene_ct += 1
if not gene_ct%10: print gene_ct, "genes out of", len(gene_list)
switch_to_db (cursor, ensembl_db_name['homo_sapiens'])
print gene_ct, len(gene_ids), gene_id, gene2stable(cursor, gene_id), get_description (cursor, gene_id)
human_exons = filter (lambda e: e.is_known==1 and e.is_coding and e.covering_exon<0, gene2exon_list(cursor, gene_id))
human_exons.sort(key=lambda exon: exon.start_in_gene)
##################################################################
for human_exon in human_exons:
tot += 1
# find all orthologous exons the human exon maps to
maps = get_maps(cursor, ensembl_db_name, human_exon.exon_id, human_exon.is_known)
if verbose:
print "\texon no.", tot, " id", human_exon.exon_id,
if not maps:
print " no maps"
print human_exon
print
if not maps:
no_maps += 1
continue
# human sequence to fasta:
seqname = "{0}:{1}:{2}".format('homo_sapiens', human_exon.exon_id, human_exon.is_known)
switch_to_db (cursor, ensembl_db_name['homo_sapiens'])
[exon_seq_id, pepseq, pepseq_transl_start, pepseq_transl_end,
left_flank, right_flank, dna_seq] = get_exon_seqs (cursor, human_exon.exon_id, human_exon.is_known)
if (not pepseq):
if verbose and human_exon.is_coding and human_exon.covering_exon <0: # this should be a master exon
print "no pep seq for", human_exon.exon_id, "coding ", human_exon.is_coding,
print "canonical: ", human_exon.is_canonical
print "length of dna ", len(dna_seq)
no_pepseq += 1
continue
# collect seq from all maps, and output them in fasta format
hassw = False
headers = []
sequences = {}
exons_per_species = {}
for map in maps:
switch_to_db (cursor, ensembl_db_name[map.species_2])
if map.similarity < min_similarity: continue
exon = map2exon(cursor, ensembl_db_name, map)
pepseq = get_exon_pepseq (cursor,exon)
if (not pepseq):
continue
if map.source == 'sw_sharp':
exon_known_code = 2
hassw = True
elif map.source == 'usearch':
exon_known_code = 3
hassw = True
else:
exon_known_code = map.exon_known_2
seqname = "{0}:{1}:{2}".format(map.species_2, map.exon_id_2, exon_known_code)
headers.append(seqname)
sequences[seqname] = pepseq
# for split exon concatenation (see below)
if not map.species_2 in exons_per_species.keys():
exons_per_species[map.species_2] = []
exons_per_species[map.species_2].append ([ map.exon_id_2, exon_known_code]);
if (len(headers) <=1 ):
if verbose: print "single species in the alignment"
no_orthologues += 1
continue
# concatenate exons from the same gene - the alignment program might go wrong otherwise
concatenated = concatenate_exons (cursor, ensembl_db_name, sequences, exons_per_species)
fasta_fnm = "{0}/{1}.fa".format( cfg.dir_path['scratch'], human_exon.exon_id)
output_fasta (fasta_fnm, sequences.keys(), sequences)
# align
afa_fnm = "{0}/{1}.afa".format( cfg.dir_path['scratch'], human_exon.exon_id)
mafftcmd = acg.generate_mafft_command (fasta_fnm, afa_fnm)
ret = commands.getoutput(mafftcmd)
if (verbose): print 'almt to', afa_fnm
# read in the alignment
inf = erropen(afa_fnm, "r")
aligned_seqs = {}
for record in SeqIO.parse(inf, "fasta"):
aligned_seqs[record.id] = str(record.seq)
inf.close()
# split back the concatenated exons
if concatenated: split_concatenated_exons (aligned_seqs, concatenated)
human_seq_seen = False
for seq_name, sequence in aligned_seqs.iteritems():
# if this is one of the concatenated seqs, split them back to two
### store the alignment as bitstring
# Generate the bitmap
bs = Bits(bin='0b' + re.sub("[^0]","1", sequence.replace('-','0')))
# The returned value of tobytes() will be padded at the end
# with between zero and seven 0 bits to make it byte aligned.
# I will end up with something that looks like extra alignment gaps, that I'll have to return
msa_bitmap = bs.tobytes()
# Retrieve information on the cognate
cognate_species, cognate_exon_id, cognate_exon_known = seq_name.split(':')
if cognate_exon_known == '2':
source = 'sw_sharp'
elif cognate_exon_known == '3':
source = 'usearch'
else:
source = 'ensembl'
if (cognate_species == 'homo_sapiens'):
human_seq_seen = True
cognate_genome_db_id = species2genome_db_id(cursor, cognate_species) # moves the cursor
switch_to_db(cursor, ensembl_db_name['homo_sapiens']) # so move it back to h**o sapiens
# Write the bitmap to the database
#if (cognate_species == 'homo_sapiens'):
if verbose: # and (source=='sw_sharp' or source=='usearch'):
print "storing"
print human_exon.exon_id, human_exon.is_known
print cognate_species, cognate_genome_db_id, cognate_exon_id, cognate_exon_known, source
print sequence
if not msa_bitmap:
print "no msa_bitmap"
continue
store_or_update(cursor, "exon_map", {"cognate_genome_db_id":cognate_genome_db_id,
"cognate_exon_id":cognate_exon_id ,"cognate_exon_known" :cognate_exon_known,
"source": source, "exon_id" :human_exon.exon_id, "exon_known":human_exon.is_known},
{"msa_bitstring":MySQLdb.escape_string(msa_bitmap)})
ok += 1
commands.getoutput("rm "+afa_fnm+" "+fasta_fnm)
if verbose: print " time: %8.3f\n" % (time()-start);
print "tot: ", tot, "ok: ", ok
print "no maps ", no_pepseq
print "no pepseq ", no_pepseq
print "no orthologues ", no_orthologues
print
def main():
# exon_id comes from the command line
if len(sys.argv) < 5:
print "Usage: %s <exon_id> <exon_known> <species> <output name> [nt]" % sys.argv[0]
exit (1)
exon_id = long(sys.argv[1])
exon_known = int(sys.argv[2])
species = sys.argv[3]
afa_name = sys.argv[4]
nt = len(sys.argv)>5 and sys.argv[5]=='nt'
######################################
db = connect_to_mysql(user="******", passwd="sqljupitersql", host="jupiter.private.bii", port=3307)
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
if not is_coding_exon(cursor, exon_id, exon_known, ensembl_db_name[species]) and not nt:
# make an empty file
cmd = "touch " + afa_name
ret = commands.getoutput(cmd)
cursor.close()
db.close()
return
######################################
if (species == 'homo_sapiens'):
[human_exon_id, human_exon_known] = [exon_id, exon_known]
ok = True
else:
# find the human exon this guy maps to
species_db_id = species2genome_db_id(cursor, species)
if (species_db_id):
[human_exon_id, human_exon_known] = find_human_cognate(cursor, ensembl_db_name, exon_id,
exon_known, species_db_id)
ok = species_db_id > 0 and human_exon_id>0
######################################
if (ok):
alignment = make_exon_alignment(cursor, ensembl_db_name, human_exon_id, human_exon_known, nt)
if (ok and alignment):
# sort the remaining species taxonomically
sorted_species = species_sort(cursor, all_species, species)
sorted_names = sort_names (sorted_species, alignment)
output_fasta (afa_name, sorted_names, alignment)
else:
# make file consisting of the original sequence only
if nt:
seq = get_exon_seqs (cursor, exon_id, exon_known, ensembl_db_name[species])[-1];
else:
seq = get_exon_pepseq (cursor, exon_id, exon_known, ensembl_db_name[species])
if seq:
alignment = {}
sequence_name = make_seq_name (cursor, ensembl_db_name, species, exon_id, exon_known, [])
alignment[sequence_name] = seq;
output_fasta (afa_name, [seq_name], alignment)
else:
# if not even the original sequence can be found, its definitely somebody else's fault;
# make an empty file
cmd = "touch " + afa_name
ret = commands.getoutput(cmd)
cursor.close()
db.close()
return
def multiple_exon_alnmt(species_list, db_info):
[local_db, ensembl_db_name] = db_info
verbose = False
db = connect_to_mysql()
cfg = ConfigurationReader()
acg = AlignmentCommandGenerator()
cursor = db.cursor()
for species in species_list:
print
print "############################"
print species
switch_to_db (cursor, ensembl_db_name[species])
gene_ids = get_gene_ids (cursor, biotype='protein_coding')
#gene_ids = get_theme_ids(cursor, cfg, 'wnt_pathway')
if not gene_ids:
print "no gene_ids"
continue
gene_ct = 0
tot = 0
ok = 0
no_maps = 0
no_pepseq = 0
no_paralogues = 0
for gene_id in gene_ids:
if verbose: start = time()
gene_ct += 1
if not gene_ct%100: print species, gene_ct, "genes out of", len(gene_ids)
if verbose:
print
print gene_id, gene2stable(cursor, gene_id), get_description (cursor, gene_id)
# get the paralogues - only the representative for the family will have this
paralogues = get_paras (cursor, gene_id)
if not paralogues:
if verbose: print "\t not a template or no paralogues"
continue
if verbose: print "paralogues: ", paralogues
# get _all_ exons
template_exons = gene2exon_list(cursor, gene_id)
if (not template_exons):
if verbose: print 'no exons for ', gene_id
continue
# find all template exons we are tracking in the database
for template_exon in template_exons:
if verbose: print template_exon.exon_id
maps = get_maps(cursor, ensembl_db_name, template_exon.exon_id,
template_exon.is_known, species=species, table='para_exon_map')
if not maps:
no_maps += 1
continue
# output to fasta:
seqname = "{0}:{1}:{2}".format('template', template_exon.exon_id, template_exon.is_known)
exon_seqs_info = get_exon_seqs (cursor, template_exon.exon_id, template_exon.is_known)
if not exon_seqs_info: continue
[exon_seq_id, pepseq, pepseq_transl_start, pepseq_transl_end,
left_flank, right_flank, dna_seq] = exon_seqs_info
if (not pepseq):
if ( template_exon.is_coding and template_exon.covering_exon <0): # this should be a master exon
print "no pep seq for", template_exon.exon_id, "coding ", template_exon.is_coding,
print "canonical: ", template_exon.is_canonical
print "length of dna ", len(dna_seq)
no_pepseq += 1
continue
tot += 1
sequences = {seqname:pepseq}
headers = [seqname]
for map in maps:
exon = map2exon(cursor, ensembl_db_name, map, paralogue=True)
pepseq = get_exon_pepseq (cursor,exon)
if (not pepseq):
continue
seqname = "{0}:{1}:{2}".format('para', map.exon_id_2, map.exon_known_2)
headers.append(seqname)
sequences[seqname] = pepseq
fasta_fnm = "{0}/{1}_{2}_{3}.fa".format( cfg.dir_path['scratch'], species, template_exon.exon_id, template_exon.is_known)
output_fasta (fasta_fnm, headers, sequences)
if (len(headers) <=1 ):
print "single species in the alignment (?)"
no_paralogues += 1
continue
# align
afa_fnm = "{0}/{1}_{2}_{3}.afa".format( cfg.dir_path['scratch'], species, template_exon.exon_id, template_exon.is_known)
mafftcmd = acg.generate_mafft_command (fasta_fnm, afa_fnm)
ret = commands.getoutput(mafftcmd)
# read in the alignment
inf = erropen(afa_fnm, "r")
if not inf:
print gene_id
continue
template_seq_seen = False
for record in SeqIO.parse(inf, "fasta"):
### store the alignment as bitstring
# Generate the bitmap
bs = Bits(bin='0b' + re.sub("[^0]","1", str(record.seq).replace('-','0')))
msa_bitmap = bs.tobytes()
# Retrieve information on the cognate
label, cognate_exon_id, cognate_exon_known = record.id.split(':')
if (label == 'template'):
template_seq_seen = True
# Write the bitmap to the database
#print "updating: ", template_exon.exon_id
store_or_update(cursor, "para_exon_map", {"cognate_exon_id" :cognate_exon_id,
"cognate_exon_known" :cognate_exon_known,
"exon_id" :template_exon.exon_id,
"exon_known" :template_exon.is_known},
{"msa_bitstring":MySQLdb.escape_string(msa_bitmap)})
inf.close()
ok += 1
commands.getoutput("rm "+afa_fnm+" "+fasta_fnm)
if verbose: print " time: %8.3f\n" % (time()-start);
outstr = species + " done \n"
outstr += "tot: %d ok: %d \n" % (tot, ok)
outstr += "no maps %d \n" % no_pepseq
outstr += "no pepseq %d \n" % no_pepseq
outstr += "no paralogues %d \n" % no_paralogues
outstr += "\n"
print outstr