def main():
if len(sys.argv) < 5:
print "Usage: %s <species> <exon_id> <exon_known> <output_name_root>" % sys.argv[0]
exit(1)
species = sys.argv[1]
exon_id = int(sys.argv[2])
exon_known = int(sys.argv[3])
output_fnm_root = sys.argv[4]
local_db = False
if local_db:
db = connect_to_mysql()
cfg = ConfigurationReader()
else:
db = connect_to_mysql (user="******", passwd="sqljupitersql", host="jupiter.private.bii", port=3307)
cfg = ConfigurationReader (user="******", passwd="sqljupitersql", host="jupiter.private.bii", port=3307)
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
sorted_species = species_sort(cursor, all_species, species)
reconstruct_alignment (cursor, cfg, ensembl_db_name, species, exon_id, exon_known, sorted_species, output_fnm_root)
cursor.close()
db.close()
return True
def main():
if len(sys.argv) < 5:
print "Usage: %s <species> <exon_id> <exon_known> <output_name_root>" % sys.argv[
0]
exit(1)
species = sys.argv[1]
exon_id = int(sys.argv[2])
exon_known = int(sys.argv[3])
output_fnm_root = sys.argv[4]
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species(cursor)
sorted_species = species_sort(cursor, all_species, species)
reconstruct_alignment(cursor, cfg, ensembl_db_name, species, exon_id,
exon_known, sorted_species, output_fnm_root)
cursor.close()
db.close()
return True
def annotate(gene_list, db_info):
#
[local_db, all_species, ensembl_db_name, species] = db_info
db = connect_to_mysql()
cfg = ConfigurationReader()
acg = AlignmentCommandGenerator()
cursor = db.cursor()
if verbose:
print "thread %s annotating %s " % (get_thread_name(), species)
if not species == "oryctolagus_cuniculus":
print "The preferred list of species is hardcoded for the rabbit. Consider modifying."
exit(1)
preferred_species = [species, "mus_musculus", "rattus_norvegicus", "homo_sapiens"]
nearest_species_list = species_sort(cursor, all_species, species)
species_list = preferred_species + filter(lambda x: x not in preferred_species, nearest_species_list)
inf = erropen("temp_out.fasta", "w")
for gene_id in gene_list:
# for gene_id in [90020]:
switch_to_db(cursor, ensembl_db_name[species])
####################
# get stable id and description of this gene
stable_id = gene2stable(cursor, gene_id)
if not gene_list.index(gene_id) % 100:
print gene_list.index(gene_id), "out of", len(gene_list)
if verbose:
print "============================================="
if verbose:
print gene_id, stable_id
####################
# find the annotation from the preferred source organism
[annot_source, orthology_type, annotation, ortho_stable_ids] = find_annotation(
cursor, ensembl_db_name, species_list, gene_id
)
if verbose:
print annot_source, "**", orthology_type, "**", annotation
###################
# find splices (for now find the canonical splice)
switch_to_db(cursor, ensembl_db_name[species])
canonical_splice = get_canonical_transl(acg, cursor, gene_id, species)
# output
if orthology_type == "self" or annotation == "none":
header = ">{0} {1}".format(stable_id, annotation)
else:
header = ">{0} {1} [by sim to {2}, {3}]".format(stable_id, annotation, annot_source, ortho_stable_ids)
print >> inf, header
print >> inf, canonical_splice
cursor.close()
db.close()
def annotate(gene_list, db_info):
#
[local_db, all_species, ensembl_db_name, species] = db_info
db = connect_to_mysql()
cfg = ConfigurationReader()
acg = AlignmentCommandGenerator()
cursor = db.cursor()
if verbose: print "thread %s annotating %s " % (get_thread_name(), species)
if not species == 'oryctolagus_cuniculus':
print 'The preferred list of species is hardcoded for the rabbit. Consider modifying.'
exit(1)
preferred_species = [
species, 'mus_musculus', 'rattus_norvegicus', 'homo_sapiens'
]
nearest_species_list = species_sort(cursor, all_species, species)
species_list = preferred_species + filter(
lambda x: x not in preferred_species, nearest_species_list)
inf = erropen("temp_out.fasta", "w")
for gene_id in gene_list:
#for gene_id in [90020]:
switch_to_db(cursor, ensembl_db_name[species])
####################
# get stable id and description of this gene
stable_id = gene2stable(cursor, gene_id)
if not gene_list.index(gene_id) % 100:
print gene_list.index(gene_id), "out of", len(gene_list)
if verbose: print "============================================="
if verbose: print gene_id, stable_id
####################
# find the annotation from the preferred source organism
[annot_source, orthology_type, annotation,
ortho_stable_ids] = find_annotation(cursor, ensembl_db_name,
species_list, gene_id)
if verbose: print annot_source, "**", orthology_type, '**', annotation
###################
# find splices (for now find the canonical splice)
switch_to_db(cursor, ensembl_db_name[species])
canonical_splice = get_canonical_transl(acg, cursor, gene_id, species)
# output
if orthology_type == 'self' or annotation == 'none':
header = ">{0} {1}".format(stable_id, annotation)
else:
header = ">{0} {1} [by sim to {2}, {3}]".format(
stable_id, annotation, annot_source, ortho_stable_ids)
print >> inf, header
print >> inf, canonical_splice
cursor.close()
db.close()
def get_template(cursor, ensembl_db_name, map_table, species, he):
template_species = None
template_seq = None
nearest_species = species_sort(cursor, list(map_table.keys()), species)[1:]
# I have a problem with the lamprey - it is an outlayer to everything else
if species == 'petromyzon_marinus':
nearest_species.reverse()
exon = Exon()
len_human_protein_seq = 1.0 * len(he.pepseq)
for nearest in nearest_species:
if not map_table[nearest][he]: continue
m = map_table[nearest][he]
if m and m.warning: continue
template_seqs = get_exon_seqs(cursor, m.exon_id_2, m.exon_known_2,
ensembl_db_name[nearest])
if not template_seqs:
template_species = None
else:
[
exon_seq_id, protein_seq, pepseq_transl_start,
pepseq_transl_end, left_flank, right_flank, dna_seq
] = template_seqs
if len(protein_seq) / len_human_protein_seq < 0.3: continue
if len_human_protein_seq / len(protein_seq) < 0.3: continue
if not left_flank or not right_flank: continue
if "XX" in protein_seq: continue
template_species = nearest
template_exon_id = m.exon_id_2
template_exon_known = m.exon_known_2
template_exon_seq_id = exon_seq_id
template_similarity_to_human = m.similarity
break
if not template_species: return None
return [
template_species, template_exon_seq_id, dna_seq, protein_seq,
template_similarity_to_human
]
def get_template (cursor, ensembl_db_name, map_table, species, he):
template_species = None
template_seq = None
nearest_species = species_sort(cursor, map_table.keys(), species)[1:]
# I have a problem with the lamprey - it is an outlayer to everything else
if species=='petromyzon_marinus':
nearest_species.reverse()
exon = Exon()
len_human_protein_seq = 1.0*len(he.pepseq)
for nearest in nearest_species:
if not map_table[nearest][he]: continue
m = map_table[nearest][he]
if m and m.warning: continue
template_seqs = get_exon_seqs (cursor, m.exon_id_2, m.exon_known_2, ensembl_db_name[nearest])
if not template_seqs:
template_species = None
else:
[exon_seq_id, protein_seq, pepseq_transl_start,
pepseq_transl_end, left_flank, right_flank, dna_seq] = template_seqs
if len(protein_seq)/len_human_protein_seq < 0.3: continue
if len_human_protein_seq/len(protein_seq) < 0.3: continue
if not left_flank or not right_flank: continue
if "XX" in protein_seq: continue
template_species = nearest
template_exon_id = m.exon_id_2
template_exon_known = m.exon_known_2
template_exon_seq_id = exon_seq_id
template_similarity_to_human = m.similarity
break
if not template_species: return None
return [template_species, template_exon_seq_id, dna_seq, protein_seq, template_similarity_to_human]
def main():
if len(sys.argv) < 5:
print "Usage: %s <species> <exon_id> <exon_known> <output_name_root>" % sys.argv[0]
exit(1)
species = sys.argv[1]
exon_id = int(sys.argv[2])
exon_known = int(sys.argv[3])
output_fnm_root = sys.argv[4]
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
sorted_species = species_sort(cursor, all_species, species)
reconstruct_alignment (cursor, cfg, ensembl_db_name, species, exon_id, exon_known, sorted_species, output_fnm_root)
cursor.close()
db.close()
return True
def find_missing_exons(human_gene_list, db_info):
#
[local_db, ensembl_db_name, method] = db_info
db = connect_to_mysql()
cfg = ConfigurationReader()
acg = AlignmentCommandGenerator()
cursor = db.cursor()
# find db ids and common names for each species db
all_species, ensembl_db_name = get_species(cursor)
# minimal acceptable similarity between exons
min_similarity = cfg.get_value('min_accptbl_exon_sim')
switch_to_db(cursor, ensembl_db_name['homo_sapiens'])
##################################################################################
# loop over human genes
gene_ct = 0
found = 0
sought = 0
unsequenced = 0
#human_gene_list.reverse()
for human_gene_id in human_gene_list:
switch_to_db(cursor, ensembl_db_name['homo_sapiens'])
# Get stable id and description of this gene -- DEBUG
human_stable = gene2stable(cursor, human_gene_id)
human_description = get_description(cursor, human_gene_id)
if verbose: print(human_gene_id, human_stable, human_description)
# progress counter
gene_ct += 1
if (not gene_ct % 10):
print("processed ", gene_ct, " out of ", len(human_gene_list),
"genes")
print("exons found: ", found, " out of ", sought, "sought")
# find all human exons for this gene that we are tracking in the database
human_exons = [
e for e in gene2exon_list(cursor, human_gene_id)
if e.covering_exon < 0 and e.is_canonical and e.is_known
]
if not human_exons:
print("\t\t no exons found")
continue
human_exons.sort(key=lambda exon: exon.start_in_gene)
for he in human_exons:
he.stable_id = exon2stable(cursor, he.exon_id)
##################################################################################
##################################################################################
# make 'table' of maps, which is either pointer to the map if it exists, or None
map_table = {}
for species in all_species:
map_table[species] = {}
for he in human_exons:
map_table[species][he] = None
#################
maps_for_exon = {}
for he in human_exons:
maps_for_exon[he] = get_maps(cursor, ensembl_db_name, he.exon_id,
he.is_known) # exon data
for m in maps_for_exon[he]:
#if m.source == 'usearch': continue
#if m.source == 'sw_sharp': continue
#if m.source == 'sw_sharp':
# print 'sw_sharp'
#if m.source == 'usearch':
# print 'usearch', m.similarity, m.species_2, m.exon_id_1, m.exon_id_2
if m.similarity < min_similarity: continue
m_previous = map_table[m.species_2][he]
if m_previous and m_previous.similarity > m.similarity:
continue
map_table[m.species_2][he] = m
# get rid of species that do not have the gene at all
for species in all_species:
one_exon_found = False
for he in human_exons:
if map_table[species][he]:
one_exon_found = True
break
if not one_exon_found:
del map_table[species]
# fill in the peptide sequence field for each human exon
# get rid of exons that appear in no other species but human (?)
bad_he = []
for he in human_exons:
one_species_found = False
he.pepseq = get_exon_pepseq(cursor, he,
ensembl_db_name['homo_sapiens'])
if len(
he.pepseq
) < 3: # can I ever get rid of all the nonsense I find in Ensembl?
bad_he.append(he)
continue
for species in list(map_table.keys()):
if species == 'homo_sapiens': continue
if map_table[species][he]:
one_species_found = True
break
if not one_species_found:
bad_he.append(he)
human_exons = [he for he in human_exons if not he in bad_he]
# keep track of nearest neighbors for each human exon
previous = {}
next = {}
prev = None
for he in human_exons:
previous[he] = prev
if prev: next[prev] = he
prev = he
next[he] = None
# fill, starting from the species that are nearest to the human
if not list(map_table.keys()):
continue # whatever
species_sorted_from_human = species_sort(cursor,
list(map_table.keys()),
species)[1:]
for species in species_sorted_from_human:
print(species)
# see which exons have which neighbors
#if verbose: print he.exon_id, species
no_left = []
no_right = []
has_both_neighbors = []
one_existing_map = None
for he in human_exons:
m = map_table[species][he]
if m and not m.warning: # the one existing map should not be a problematic one
one_existing_map = m
continue
prev = previous[he]
nxt = next[he]
if prev and nxt and map_table[species][prev] and map_table[
species][nxt]:
has_both_neighbors.append(he)
elif not prev or not map_table[species][prev]:
no_left.append(he)
elif not nxt or not map_table[species][nxt]:
no_right.append(he)
if not one_existing_map: continue # this shouldn't happen
if not has_both_neighbors and not no_left and not no_right:
continue
# what is the gene that we are talking about?
exon_id = one_existing_map.exon_id_2
is_known = one_existing_map.exon_known_2
gene_id = exon_id2gene_id(cursor, ensembl_db_name[species],
exon_id, is_known)
# is it mitochondrial?
mitochondrial = is_mitochondrial(cursor, gene_id,
ensembl_db_name[species])
# where is the gene origin (position on the sequence)
gene_coords = get_gene_coordinates(cursor, gene_id,
ensembl_db_name[species])
if not gene_coords: continue
[gene_seq_region_id, gene_start, gene_end,
gene_strand] = gene_coords
# fill in exons that have both neighbors:
# human exon functions as a coordinate here
for he in has_both_neighbors:
# get template (known exon from the nearest species)
template_info = get_template(cursor, ensembl_db_name,
map_table, species, he)
if not template_info: continue
# previous_ and next_seq_region are of the type Seq_Region defined on the top of the file
# get previous region
prev_seq_region = get_neighboring_region(
cursor, ensembl_db_name, map_table, species, gene_coords,
he, previous[he])
if not prev_seq_region: continue
# get following region
next_seq_region = get_neighboring_region(
cursor, ensembl_db_name, map_table, species, gene_coords,
he, next[he])
if not next_seq_region: continue
sought += 1
reply = find_NNN(cursor, ensembl_db_name, cfg, acg, he,
maps_for_exon[he], species, gene_id,
gene_coords, prev_seq_region, next_seq_region,
template_info, mitochondrial, method)
if reply == 'NNN':
unsequenced += 1
# work backwards
# use the last known region on the left as the bound
no_left.reverse()
next_seq_region = None
for he in no_left:
m = map_table[species][he]
# check first if we haave already looked into this, and found incomplete region
#if m and m.warning: continue
# get template (known exon from the nearest species)
template_info = get_template(cursor, ensembl_db_name,
map_table, species, he)
if not template_info: continue
# get following region
if not next_seq_region:
next_seq_region = get_neighboring_region(
cursor, ensembl_db_name, map_table, species,
gene_coords, he, next[he])
if not next_seq_region: continue
# otherwise it is the last thing we found
# the previous region is eyeballed from the next on
# the previous and the next region frame the search region
prev_seq_region = left_region(next_seq_region,
MAX_SEARCH_LENGTH)
sought += 1
reply = find_NNN(cursor, ensembl_db_name, cfg, acg, he,
maps_for_exon[he], species, gene_id,
gene_coords, prev_seq_region, next_seq_region,
template_info, mitochondrial, method)
if reply == 'NNN':
unsequenced += 1
# repeat the whole procedure on the right
prev_seq_region = None
for he in no_right:
m = map_table[species][he]
# check first if we haave already looked into this, and found incomplete region
#if m and m.warning: continue
# get template (known exon from the nearest species)
template_info = get_template(cursor, ensembl_db_name,
map_table, species, he)
if not template_info: continue
# get following region
if not prev_seq_region:
prev_seq_region = get_neighboring_region(
cursor, ensembl_db_name, map_table, species,
gene_coords, he, previous[he])
if not prev_seq_region: continue
# otherwise it is the last thing we found
# the following region is eyeballed from the previous
next_seq_region = right_region(prev_seq_region,
MAX_SEARCH_LENGTH)
sought += 1
reply = find_NNN(cursor, ensembl_db_name, cfg, acg, he,
maps_for_exon[he], species, gene_id,
gene_coords, prev_seq_region, next_seq_region,
template_info, mitochondrial, method)
if reply == 'NNN':
unsequenced += 1
print(species, "sought", sought, " unseq", unsequenced)
def find_missing_exons(human_gene_list, db_info):
#
[local_db, ensembl_db_name, method] = db_info
db = connect_to_mysql()
cfg = ConfigurationReader()
acg = AlignmentCommandGenerator()
cursor = db.cursor()
# find db ids and common names for each species db
all_species, ensembl_db_name = get_species (cursor)
# minimal acceptable similarity between exons
min_similarity = cfg.get_value('min_accptbl_exon_sim')
switch_to_db (cursor, ensembl_db_name['homo_sapiens'])
##################################################################################
# loop over human genes
gene_ct = 0
found = 0
sought = 0
unsequenced = 0
#human_gene_list.reverse()
for human_gene_id in human_gene_list:
switch_to_db (cursor, ensembl_db_name['homo_sapiens'])
# Get stable id and description of this gene -- DEBUG
human_stable = gene2stable (cursor, human_gene_id)
human_description = get_description(cursor, human_gene_id)
if verbose: print human_gene_id, human_stable, human_description
# progress counter
gene_ct += 1
if (not gene_ct%10):
print "processed ", gene_ct, " out of ", len(human_gene_list), "genes"
print "exons found: ", found, " out of ", sought, "sought"
# find all human exons for this gene that we are tracking in the database
human_exons = [e for e in gene2exon_list(cursor, human_gene_id)
if e.covering_exon < 0 and e.is_canonical and e.is_known]
if not human_exons:
print "\t\t no exons found"
continue
human_exons.sort(key=lambda exon: exon.start_in_gene)
for he in human_exons:
he.stable_id = exon2stable (cursor, he.exon_id)
##################################################################################
##################################################################################
# make 'table' of maps, which is either pointer to the map if it exists, or None
map_table = {}
for species in all_species:
map_table[species] = {}
for he in human_exons:
map_table[species][he] = None
#################
maps_for_exon = {}
for he in human_exons:
maps_for_exon[he] = get_maps(cursor, ensembl_db_name, he.exon_id, he.is_known) # exon data
for m in maps_for_exon[he]:
#if m.source == 'usearch': continue
#if m.source == 'sw_sharp': continue
#if m.source == 'sw_sharp':
# print 'sw_sharp'
#if m.source == 'usearch':
# print 'usearch', m.similarity, m.species_2, m.exon_id_1, m.exon_id_2
if m.similarity < min_similarity: continue
m_previous = map_table[m.species_2][he]
if m_previous and m_previous.similarity > m.similarity:
continue
map_table[m.species_2][he] = m
# get rid of species that do not have the gene at all
for species in all_species:
one_exon_found = False
for he in human_exons:
if map_table[species][he]:
one_exon_found = True
break
if not one_exon_found:
del map_table[species]
# fill in the peptide sequence field for each human exon
# get rid of exons that appear in no other species but human (?)
bad_he = []
for he in human_exons:
one_species_found = False
he.pepseq = get_exon_pepseq (cursor, he, ensembl_db_name['homo_sapiens'])
if len (he.pepseq) < 3: # can I ever get rid of all the nonsense I find in Ensembl?
bad_he.append(he)
continue
for species in map_table.keys():
if species =='homo_sapiens': continue
if map_table[species][he]:
one_species_found = True
break
if not one_species_found:
bad_he.append(he)
human_exons = filter (lambda he: not he in bad_he, human_exons)
# keep track of nearest neighbors for each human exon
previous = {}
next = {}
prev = None
for he in human_exons:
previous[he] = prev
if prev: next[prev] = he
prev = he
next[he] = None
# fill, starting from the species that are nearest to the human
if not map_table.keys():
continue # whatever
species_sorted_from_human = species_sort(cursor,map_table.keys(),species)[1:]
for species in species_sorted_from_human:
print species
# see which exons have which neighbors
#if verbose: print he.exon_id, species
no_left = []
no_right = []
has_both_neighbors = []
one_existing_map = None
for he in human_exons:
m = map_table[species][he]
if m and not m.warning: # the one existing map should not be a problematic one
one_existing_map = m
continue
prev = previous[he]
nxt = next[he]
if prev and nxt and map_table[species][prev] and map_table[species][nxt]:
has_both_neighbors.append(he)
elif not prev or not map_table[species][prev]:
no_left.append(he)
elif not nxt or not map_table[species][nxt]:
no_right.append(he)
if not one_existing_map: continue # this shouldn't happen
if not has_both_neighbors and not no_left and not no_right: continue
# what is the gene that we are talking about?
exon_id = one_existing_map.exon_id_2
is_known = one_existing_map.exon_known_2
gene_id = exon_id2gene_id (cursor, ensembl_db_name[species], exon_id, is_known)
# is it mitochondrial?
mitochondrial = is_mitochondrial(cursor, gene_id, ensembl_db_name[species])
# where is the gene origin (position on the sequence)
gene_coords = get_gene_coordinates (cursor, gene_id, ensembl_db_name[species])
if not gene_coords: continue
[gene_seq_region_id, gene_start, gene_end, gene_strand] = gene_coords
# fill in exons that have both neighbors:
# human exon functions as a coordinate here
for he in has_both_neighbors:
# get template (known exon from the nearest species)
template_info = get_template (cursor, ensembl_db_name,
map_table, species, he)
if not template_info: continue
# previous_ and next_seq_region are of the type Seq_Region defined on the top of the file
# get previous region
prev_seq_region = get_neighboring_region (cursor, ensembl_db_name,
map_table, species, gene_coords, he, previous[he])
if not prev_seq_region: continue
# get following region
next_seq_region = get_neighboring_region (cursor, ensembl_db_name,
map_table, species, gene_coords, he, next[he])
if not next_seq_region: continue
sought += 1
reply = find_NNN (cursor, ensembl_db_name, cfg, acg, he, maps_for_exon[he],
species, gene_id, gene_coords, prev_seq_region,
next_seq_region, template_info, mitochondrial, method)
if reply=='NNN':
unsequenced += 1
# work backwards
# use the last known region on the left as the bound
no_left.reverse()
next_seq_region = None
for he in no_left:
m = map_table[species][he]
# check first if we haave already looked into this, and found incomplete region
#if m and m.warning: continue
# get template (known exon from the nearest species)
template_info = get_template (cursor, ensembl_db_name, map_table, species, he)
if not template_info: continue
# get following region
if not next_seq_region:
next_seq_region = get_neighboring_region (cursor, ensembl_db_name, map_table,
species, gene_coords, he, next[he])
if not next_seq_region: continue
# otherwise it is the last thing we found
# the previous region is eyeballed from the next on
# the previous and the next region frame the search region
prev_seq_region = left_region (next_seq_region, MAX_SEARCH_LENGTH)
sought += 1
reply = find_NNN (cursor, ensembl_db_name, cfg, acg, he, maps_for_exon[he],
species, gene_id, gene_coords, prev_seq_region, next_seq_region,
template_info, mitochondrial, method)
if reply=='NNN':
unsequenced += 1
# repeat the whole procedure on the right
prev_seq_region = None
for he in no_right:
m = map_table[species][he]
# check first if we haave already looked into this, and found incomplete region
#if m and m.warning: continue
# get template (known exon from the nearest species)
template_info = get_template (cursor, ensembl_db_name,
map_table, species, he)
if not template_info: continue
# get following region
if not prev_seq_region:
prev_seq_region = get_neighboring_region (cursor, ensembl_db_name, map_table,
species, gene_coords, he, previous[he])
if not prev_seq_region: continue
# otherwise it is the last thing we found
# the following region is eyeballed from the previous
next_seq_region = right_region (prev_seq_region, MAX_SEARCH_LENGTH)
sought += 1
reply = find_NNN (cursor, ensembl_db_name, cfg, acg, he, maps_for_exon[he],
species, gene_id, gene_coords, prev_seq_region, next_seq_region,
template_info, mitochondrial, method)
if reply=='NNN':
unsequenced += 1
print species, "sought", sought, " unseq", unsequenced
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 main():
if len(sys.argv) < 2:
print("usage: %s <gene symbol> [trivial] [prepend]" % sys.argv[0])
print(
"trivial = use trivial species name; prepend = prepend gene name")
exit()
gene_name = sys.argv[1]
trivial = "trivial" in sys.argv
prepend = "prepend" in sys.argv # prepends geen synbol to gene name
ref_species = 'homo_sapiens' # the orthologue table is filled only here, for the moment
out_fasta = f"{gene_name}.orthos.fasta"
out_afa = f"{gene_name}.orthos.afa"
tmpfile = "tmp.fa"
logfile = "tmp.log"
for fnm in [out_fasta, out_afa, tmpfile, logfile]:
if os.path.exists(fnm): os.remove(fnm)
home = os.getcwd()
db = connect_to_mysql(Config.mysql_conf_file)
cursor = db.cursor()
qry = "select ensembl_gene_id from identifier_maps.hgnc where approved_symbol='%s'" % gene_name
ensembl_stable_gene_id = hard_landing_search(cursor, qry)[0][0]
[all_species, ensembl_db_name] = get_species(cursor)
# species_sort(cursor, all_species, 'homo_sapiens')
# exit()
switch_to_db(cursor, ensembl_db_name[ref_species])
qry = "select gene_id from gene where stable_id='%s'" % ensembl_stable_gene_id
gene_id = hard_landing_search(cursor, qry)[0][0]
ref_stable_transl_id = gene2stable_canon_transl_id(
cursor, gene_id, ensembl_db_name[ref_species])
write_to_fasta(home, ref_species, ref_stable_transl_id, tmpfile, logfile,
out_fasta)
print(gene_name, ensembl_stable_gene_id, gene_id, ref_stable_transl_id)
species_in_the_almt = [ref_species]
qry = "select cognate_gene_id, cognate_genome_db_id from orthologues where gene_id=%d" % gene_id
for line in error_intolerant_search(cursor, qry):
[cognate_gene_id, cognate_genome_db_id] = line
qry = f"select db_name from exolocator_meta.db_names where genome_db_id={cognate_genome_db_id}"
db_name = hard_landing_search(cursor, qry)[0][0]
stable_transl_id = gene2stable_canon_transl_id(cursor, cognate_gene_id,
db_name)
species = db_name.split("core")[0].rstrip("_")
if species not in all_species: continue
print(db_name, species, cognate_gene_id, stable_transl_id)
ok = write_to_fasta(home, species, stable_transl_id, tmpfile, logfile,
out_fasta)
if ok: species_in_the_almt.append(species)
if os.path.exists(tmpfile): os.remove(tmpfile)
cmd = f"{Config.muscle} -in {out_fasta} -out tmp.afa"
subprocess.call(["bash", "-c", cmd])
species_sorted = species_sort(cursor, species_in_the_almt, ref_species)
trivial_names = get_trivial(cursor, species_sorted) if trivial else None
name_prefix = gene_name if prepend else None
reorder_seqs('tmp.afa', species_sorted, out_afa, trivial_names,
name_prefix)
if os.path.exists('tmp.afa'): os.remove('tmp.afa')
cursor.close()
db.close()
return True