def parse_text(self, text_query):
complement_prefix = 'Complement of '
for line in text_query.splitlines():
if line.startswith(complement_prefix):
line = line[len(complement_prefix):]
data = line.strip().split()
if len(data) == 4:
chrom, pos, ref, alt = data
if chrom.startswith('chr'):
chrom = chrom[3:]
items = bdb.get_genomic_muts(chrom, pos, ref, alt)
if not items:
line = complement_prefix + line
items = bdb.get_genomic_muts(chrom, pos, complement(ref),
complement(alt))
elif len(data) == 2:
gene, mut = [x.upper() for x in data]
items = get_protein_muts(gene, mut)
else:
self.badly_formatted.append(line)
continue
self.add_mutation_items(items, line)
def parse_vcf(self, vcf_file):
for line in vcf_file:
line = line.decode('latin1').strip()
if line.startswith('#'):
continue
data = line.split()
if len(data) < 5:
if not line: # if we reached end of the file
break
self.badly_formatted.append(line)
continue
chrom, pos, var_id, ref, alts = data[:5]
if chrom.startswith('chr'):
chrom = chrom[3:]
alts = alts.split(',')
for alt in alts:
items = bdb.get_genomic_muts(chrom, pos, ref, alt)
chrom = 'chr' + chrom
parsed_line = ' '.join((chrom, pos, ref, alt)) + '\n'
self.add_mutation_items(items, parsed_line)
# we don't have queries in our format for vcf files:
# those need to be built this way
self.query += parsed_line
def mutation(self, chrom, dna_pos, dna_ref, dna_alt):
"""Rest API endpoint.
Stop codon mutations are not considered."""
_, filter_manager = self._make_filters()
if chrom.startswith('chr'):
chrom = chrom[3:]
items = bdb.get_genomic_muts(chrom, dna_pos, dna_ref, dna_alt)
raw_mutations = filter_manager.apply([item.mutation for item in items])
parsed_mutations = represent_mutations(raw_mutations, filter_manager)
return jsonify(parsed_mutations)
def autocomplete_mutation(query, limit=None):
"""Returns: (autocompletion_mutation_results, are_there_more)"""
# TODO: rewriting this into regexp-based set of function may increase readability
# TODO: use limit to restrict queries
query = query.upper().strip()
data = query.split()
items = []
messages = []
if len(data) == 1:
if query.startswith('CHR'):
messages += json_message(
'Awaiting for mutation in <code>{chrom} {pos} {ref} {alt}</code> format'
)
gene = data[0].strip()
if gene_exists(gene):
messages += json_message(
'Awaiting for <code>{ref}{pos}{alt}</code> - expecting mutation in <code>{gene} {ref}{pos}{alt}</code> format'
)
else:
# return json_message('Gene %s not found in the database' % gene)
pass
elif len(data) == 4:
chrom, pos, ref, alt = data
if not query.startswith('CHR'):
return []
chrom = chrom[3:]
try:
items = bdb.get_genomic_muts(chrom, pos, ref, alt)
# maybe an interesting mutation is located on the other strand
if not items:
query = 'complement of ' + query
items = bdb.get_genomic_muts(chrom, pos, complement(ref),
complement(alt))
items = prepare_items(items, query, 'nucleotide mutation')
except ValueError:
return json_message(
'Did you mean to search for mutation with <code>{chrom} {pos} {ref} {alt}</code> format?'
' The <code>{pos}</code> should be an integer.')
elif len(data) == 3:
if not query.startswith('CHR'):
return []
return json_message(
'Awaiting for mutation in <code>{chrom} {pos} {ref} {alt}</code> format'
)
elif len(data) == 2:
gene, mut = data
result = match_aa_mutation(gene, mut, query)
items = [r for r in result if r['type'] != 'message']
messages = [r for r in result if r['type'] == 'message']
if query.startswith('CHR') and mut.isnumeric():
messages += json_message(
'Awaiting for mutation in <code>{chrom} {pos} {ref} {alt}</code> format'
)
if not limit:
limit = len(items)
return items[:limit] + messages, len(items) > limit