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refine gene symbols #69
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@oschwengers
oschwengers committed Aug 25, 2021
1 parent e709d00 commit 539137b
Showing 1 changed file with 85 additions and 15 deletions.
100 changes: 85 additions & 15 deletions bakta/features/annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,19 @@
log = logging.getLogger('ANNOTATION')


RE_CONTIG = re.compile(r'\s+contig\s*', flags=re.IGNORECASE)
RE_HOMOLOG = re.compile(r'\shomolog(?: (\d+))?', flags=re.IGNORECASE)
RE_PUTATIVE = re.compile(r'(potential|possible|probable|predicted)', flags=re.IGNORECASE)
RE_MULTIWHITESPACE = re.compile(r'\s{2,}')
RE_NODE = re.compile(r'NODE_', flags=re.IGNORECASE)
RE_POTENTIAL_CONTIG_NAME = re.compile(r'(genome|shotgun)', flags=re.IGNORECASE)
RE_NO_LETTERS = re.compile(r'[^A-Za-z]')

RE_PROTEIN_CONTIG = re.compile(r'\s+contig\s*', flags=re.IGNORECASE)
RE_PROTEIN_HOMOLOG = re.compile(r'\shomolog(?: (\d+))?', flags=re.IGNORECASE)
RE_PROTEIN_PUTATIVE = re.compile(r'(potential|possible|probable|predicted)', flags=re.IGNORECASE)
RE_PROTEIN_NODE = re.compile(r'NODE_', flags=re.IGNORECASE)
RE_PROTEIN_POTENTIAL_CONTIG_NAME = re.compile(r'(genome|shotgun)', flags=re.IGNORECASE)
RE_PROTEIN_NO_LETTERS = re.compile(r'[^A-Za-z]')
RE_PROTEIN_SYMBOL = re.compile(r'[A-Z][a-z]{2}[A-Z][0-9]?')

RE_GENE_CAPITALIZED = re.compile(r'^[A-Z].+', flags=re.DOTALL)
RE_GENE_SUSPECT_CHARS = re.compile(r'[\?]', flags=re.DOTALL)
RE_GENE_SYMBOL = re.compile(r'[a-z]{3}[A-Z][?:0-9]+')


def combine_annotation(feature):
Expand Down Expand Up @@ -73,8 +79,9 @@ def combine_annotation(feature):
db_xrefs.add(expert_db_xref)
rank = expert_rank

feature['gene'] = gene
if(gene):
feature['gene'] = gene
revise_cds_gene_symbol(feature)

if(product):
feature['product'] = product
Expand Down Expand Up @@ -364,6 +371,69 @@ def calc_sorf_annotation_score(sorf):
return score


def revise_cds_gene_symbol(feature):
raw_gene = feature.get('gene', '')

raw_genes = raw_gene.replace('/', ',').split(',') # replace slashes and split raw genes

revised_genes = []
for gene in raw_genes:
old_gene = gene
if(RE_GENE_SUSPECT_CHARS.search(gene)): # check for suspect characters -> remove gene symbol
log.info('fix gene: remove gene symbol containing suspect chars. old=%s', old_gene)
continue

old_gene = gene
if('gene' in gene): # remove gene literal
gene = gene.replace('gene', '')
log.info('fix gene: remove gene literal. new=%s, old=%s', gene, old_gene)

old_gene = gene
if(gene[-1] == '-'): # remove orphan hyphen
gene = gene[:-1]
log.info('fix gene: remove orphan hypen. new=%s, old=%s', gene, old_gene)

old_gene = gene
if(RE_MULTIWHITESPACE.search(gene)): # squeeze multiple whitespaces
gene = RE_MULTIWHITESPACE.sub(' ', gene)
log.info('fix gene: squeeze multiple whitespaces. new=%s, old=%s', gene, old_gene)

old_gene = gene
gene = gene.strip() # trim leading/trailing whitespaces
if(gene != old_gene):
log.info('fix gene: trim leading/trailing whitespace. new=%s, old=%s', gene, old_gene)

old_gene = gene
if(RE_GENE_CAPITALIZED.fullmatch(gene)): # TODO lowercase first character
gene = gene[0].lower() + gene[1:]
log.info('fix gene: lowercase first char. new=%s, old=%s', gene, old_gene)

if(len(gene) >= 3):
if(len(gene) <= 12):
revised_genes.append(gene)
else:
old_gene = gene
for part in gene.split(' '): # try to extract valid gene symbols
m = RE_GENE_SYMBOL.fullmatch(part)
if(m):
symbol = m[0]
revised_genes.append(symbol)
log.info('fix gene: extract symbol from protein name. new=%s, old=%s', symbol, old_gene)
else:
m = RE_PROTEIN_SYMBOL.fullmatch(part) # extract protein names
if(m):
symbol = m[0]
symbol = symbol[0].lower() + symbol[1:]
revised_genes.append()

if(len(revised_genes) == 0):
feature['gene'] = None
elif(len(revised_genes) == 1):
feature['gene'] = revised_genes[0]
else:
feature['gene'] = ','.join(revised_genes)


def revise_cds_product(feature):
"""Revise product name for INSDC compliant submissions"""
product = feature['product']
Expand All @@ -379,19 +449,19 @@ def revise_cds_product(feature):
log.info('fix product: remove = character. new=%s, old=%s', product, old_product)

old_product = product
if(RE_CONTIG.search(product)):
if(RE_PROTEIN_CONTIG.search(product)):
product = bc.HYPOTHETICAL_PROTEIN
feature['hypothetical'] = True
log.info('fix product: remove product containing "contig". new=%s, old=%s', product, old_product)

old_product = product
if(RE_HOMOLOG.search(product)): # replace Homologs
product = RE_HOMOLOG.sub('-like protein', product)
if(RE_PROTEIN_HOMOLOG.search(product)): # replace Homologs
product = RE_PROTEIN_HOMOLOG.sub('-like protein', product)
log.info('fix product: replace Homolog. new=%s, old=%s', product, old_product)

old_product = product
if(RE_PUTATIVE.search(product)): # replace putative synonyms)
product = RE_PUTATIVE.sub('putative', product)
if(RE_PROTEIN_PUTATIVE.search(product)): # replace putative synonyms)
product = RE_PROTEIN_PUTATIVE.sub('putative', product)
log.info('fix product: replace putative synonyms. new=%s, old=%s', product, old_product)

old_product = product
Expand All @@ -405,9 +475,9 @@ def revise_cds_product(feature):
log.info('fix product: trim leading/trailing whitespace. new=%s, old=%s', product, old_product)

if(
RE_NODE.search(product) or # potential contig name (SPAdes)
RE_POTENTIAL_CONTIG_NAME.search(product) or # potential contig name (SPAdes)
RE_NO_LETTERS.fullmatch(product) # no letters -> set to Hypothetical
RE_PROTEIN_NODE.search(product) or # potential contig name (SPAdes)
RE_PROTEIN_POTENTIAL_CONTIG_NAME.search(product) or # potential contig name (SPAdes)
RE_PROTEIN_NO_LETTERS.fullmatch(product) # no letters -> set to Hypothetical
): # remove suspect products and mark as hypothetical
product = bc.HYPOTHETICAL_PROTEIN
feature['hypothetical'] = True
Expand Down

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