def do_queries_for_lvg(lvg, strict=False):
pmids = set()
unusable = 0
for variant in lvg.variants['p'].values():
try:
comp = VariantComponents(variant)
result = db.search(comp, lvg.gene_name, strict=strict)
if result:
print('@@@ RESULTS for {gene} + {ref}|{pos}'.format(
gene=lvg.gene_name, ref=comp.ref, pos=comp.pos))
for item in result:
pmids.add(item['PMID'])
except Exception as error:
unusable += 1
print('[%s] %i p-vars (%i unusable)' %
(lvg.seqvar, len(lvg.hgvs_p), unusable))
for pmid in pmids:
print('\t* %s' % pmid)
print()
return len(pmids)
def get_posedits_for_seqvar(seqvar):
posedits = []
try:
comp = VariantComponents(seqvar)
except RejectedSeqVar as error:
log.debug(error)
return []
# 1) Official
official_term = quoted_posedit(comp)
if official_term:
posedits.append(official_term)
# 2) Slang
try:
for slang_term in comp.posedit_slang:
slang_term = '"%s"' % slang_term
if slang_term != official_term:
posedits.append(slang_term)
except NotImplementedError as error:
# silently omit (but log) any seqvar with an edittype we don't currently support
log.debug(error)
return posedits
def search_aminoDBs(gene, achg):
print('[%s]' % achg)
comp = VariantComponents(aminochange=achg)
if not comp:
print('[%s] INVALID Amino Change' % achg)
return
print('[%s] Posedit: %s' % (achg, comp.posedit))
print('[%s] Slang: %r' % (achg, comp.posedit_slang))
gene_id = GeneID(gene)
print('[%s] Gene: %s (ID: %i)' % (achg, gene, gene_id))
#results = cvdb.search(comp, gene_id, strict=False)
#print('[%s] Clinvar LOOSE matches: %r' % (achg, results))
results = cvdb.search(comp, gene_id, strict=True)
print('[%s] Clinvar STRICT matches: %i' % (achg, len(results)))
for res in results:
print('[%s]' % achg, res['PMID'], res['HGVS'], res['VariationID'], res['GeneSymbol'], res['Ref'], res['Pos'], res['Alt'])
results = pubdb.search_proteins(comp, gene_id)
print('[%s] PubtatorDB matches: %i' % (achg, len(results)))
for res in results:
print(res)
def components_or_None(hgvs_p):
try:
comp = VariantComponents(Variant(hgvs_p))
if comp.ref != '':
return comp
except (TypeError, RejectedSeqVar, CriticalHgvsError):
# either the hgvs_p did not parse (Variant returned None) or it has incomplete edit info.
pass
return None
def find_variant_in_clinvar(lex):
for seqvar in lex.seqvars:
try:
comp = VariantComponents(seqvar)
if ClinvarVariationID('%s' % seqvar):
return seqvar
except RejectedSeqVar:
pass
return None
def process_hgvs_through_pubtator(hgvs_text):
print()
print('[%s]' % hgvs_text)
lex = LVG(hgvs_text)
edittype = VariantComponents(lex.seqvar).edittype
if edittype not in ['SUB', 'DEL', 'INS', 'FS', 'INDEL']:
print('[%s] Cannot process edit type %s; skipping' %
(hgvs_text, edittype))
return None
try:
gene_id = GeneID(lex.gene_name)
except TypeError:
# no gene_name? it happens.
gene_id = None
print('[%s]' % hgvs_text, lex.gene_name, '(Gene ID: %s)' % gene_id)
pmids = set()
for seqtype in lex.variants:
for seqvar in lex.variants[seqtype]:
try:
components = VariantComponents(seqvar)
except RejectedSeqVar:
print('[%s] Rejected sequence variant: %r' %
(hgvs_text, seqvar))
continue
print('[%s]' % hgvs_text, seqtype, components)
if seqtype == 'p':
results = pubtator_db.search_proteins(components, gene_id)
else:
results = pubtator_db.search_m2p(components, gene_id)
for res in results:
pmids.add(res['PMID'])
return pmids
def pubtator_lex_to_pmid(lex, gene_name=None):
""" Takes an LVG object ("lex") (metavariant.VariantLVG) and uses each
variant found in lex.variants to do a search in PubTator for associated PMIDs.
Returns a dictionary of results mapping VariantComponents objects to PMIDs found -- i.e.:
{ hgvs_text: {'comp': VariantComponents object,
'pmids': [<pmids>]
}
:param lex: lexical variant object (metavariant.VariantLVG)
:return: dictionary of results
"""
gene_id = None
if gene_name:
gene_id = GeneID(gene_name)
else:
try:
gene_name = lex.gene_name
gene_id = GeneID(lex.gene_name)
except TypeError:
# no gene_name? it happens -- but our results will be basically bunk without it.
return []
log.info('[%s] %s (Gene ID: %s)', lex.seqvar, gene_name, gene_id)
pmids = set()
for seqtype in lex.variants:
for seqvar in lex.variants[seqtype].values():
try:
components = VariantComponents(seqvar)
except RejectedSeqVar:
log.debug('[%s] Rejected sequence variant: %r' %
(lex.seqvar, seqvar))
continue
log.info('[%s] [[%s]] %s', lex.seqvar, seqvar, components)
try:
if seqtype == 'p':
results = pubtator_db.search_proteins(components, gene_id)
else:
results = pubtator_db.search_m2p(components, gene_id)
for res in results:
pmids.add(res['PMID'])
except PubtatorDBError as error:
log.info('[%s] (%s) %r', lex.seqvar, seqvar, error)
return list(pmids)
def parse_components(components):
for name, re_patt in list(component_patterns.items()):
match = re_patt.search(components)
if match:
comp_dict = match.groupdict()
# verify that this is an entry that actually helps us; remove any
# entry that doesn't have a valid position (Pos).
if comp_dict['Pos'].strip() == '':
write_missing_position(comp_dict)
return None
components = VariantComponents(**comp_dict)
return components.to_mysql_dict()
if components.startswith('rs'):
return {'RS': components, 'EditType': 'rs'}
else:
return None
def query(hgvs_text=''):
""" Runs all of the relevant search queries after producing a lex object from input hgvs_text """
# Normalize all requests to a GET with hgvs_text having no gene name.
if request.method == 'POST':
hgvs_text = strip_gene_name_from_hgvs_text(
request.form.get('hgvs_text', '').strip())
return redirect('/query/%s' % hgvs_text, code=302)
else:
if strip_gene_name_from_hgvs_text(hgvs_text) != hgvs_text:
return redirect('/query/%s' %
strip_gene_name_from_hgvs_text(hgvs_text),
code=302)
hgvs_text = hgvs_text.strip()
try:
lex = LVG(hgvs_text)
except CriticalHgvsError as error:
return render_template('demo.html', error_msg='%r' % error)
# GENE INFO: nice info to have at hand (e.g. medgen url) if we know the gene name for this variant.
if lex.gene_name:
gene_info = GeneInfo(gene_name=lex.gene_name)
else:
gene_info = None
# CLINVAR INFO: nice info to have at hand if we can look up the variation ID for given hgvs_text.
clinvar_info = ClinVarInfo(hgvs_text)
# CITATION TABLE: handles all the heavy lifting of hgvs2pmid lookups and arrange citations by PMID.
citation_table = CitationTable(lex)
# LOVD URL: link to search in a relevant LOVD instance, if we know of one.
comp = VariantComponents(lex.seqvar)
lovd_url = get_lovd_url(lex.gene_name, comp)
return render_template('query.html',
lex=lex,
lovd_url=lovd_url,
citation_table=citation_table,
clinvar=clinvar_info,
gene=gene_info,
found_in_clinvar_example_tables=None)
def clinvar_lex_to_pmid(lex):
""" Takes a "lex" object (metavariant.VariantLVG) and uses each variant found in
lex.variants to do a search in Clinvar for associated PMIDs.
Returns a list of PMIDs.
:param lex: lexical variant object (metavariant.VariantLVG)
:return: list of pmids found in Clinvar
"""
pmids = set()
for seqtype in lex.variants:
for seqvar in lex.variants[seqtype].values():
# throw away sequence variants without enough information
try:
VariantComponents(seqvar)
except RejectedSeqVar:
log.debug('[%s] Rejected sequence variant: %r' %
(lex.seqvar, seqvar))
continue
for pmid in ClinvarPubmeds('%s' % seqvar):
pmids.add(pmid)
return list(pmids)
def hgvs_to_pmid_results_dict(hgvs_text):
print()
print('[%s]' % hgvs_text)
lex = LVG(hgvs_text)
edittype = VariantComponents(lex.seqvar).edittype
if edittype not in ['SUB', 'DEL', 'INS', 'FS', 'INDEL']:
print('[%s] Cannot process edit type %s; skipping' %
(hgvs_text, edittype))
return None
try:
gene_id = GeneID(lex.gene_name)
except TypeError:
# no gene_name? it happens.
gene_id = None
print('[%s]' % hgvs_text, lex.gene_name, '(Gene ID: %s)' % gene_id)
pmid_results = {}
pmid_results['PubTator'] = PubtatorHgvs2Pmid(lex)
pmid_results['ClinVar'] = ClinvarHgvs2Pmid(lex)
return pmid_results
def pubtator_results_for_seqvar(seqvar_or_hgvs_text, gene_id):
""" Takes a SequenceVariant or hgvs_text string.
Returns a dictionary of results mapping hgvs_text to a list of results from pubtator, i.e.:
{ hgvs_text: [ <dictionaries representing matching results from pubtator> ] }
:param seqvar_or_hgvs_text: hgvs_text or SequenceVariant object
:param gene_id: id of gene associated with variant (required)
:return: dictionary of results
:raises: RejectedSeqVar, PubtatorDBError
"""
seqvar = Variant(seqvar_or_hgvs_text)
hgvs_text = '%s' % seqvar
result = {hgvs_text: []}
components = VariantComponents(seqvar)
if seqvar.type == 'p':
result[hgvs_text] = pubtator_db.search_proteins(components, gene_id)
else:
result[hgvs_text] = pubtator_db.search_m2p(components, gene_id)
return result
def test_insert(self):
var_c = Variant(hgvs_c['INS'])
comp = VariantComponents(var_c)
pass
def test_simple_substitution(self):
var_c = Variant(hgvs_c['SUB'])
comp = VariantComponents(var_c)
pass
def test_duplication(self):
var_c = Variant(hgvs_c['DUP'])
comp = VariantComponents(var_c)
pass
def test_indel(self):
var_n = Variant(hgvs_n['INDEL'])
comp = VariantComponents(var_n)
pass
def test_frameshift(self):
var_p = Variant(hgvs_p['FS'])
comp = VariantComponents(var_p)
pass
def test_deletion(self):
var_g = Variant(hgvs_g['DEL'])
comp = VariantComponents(var_g)
pass