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Fix common INSDC submission errors on feature products #334

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merged 6 commits into from
Oct 10, 2024
Merged

Fix common INSDC submission errors on feature products #334

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ce58ef1
add whitespace replacement
oschwengers Oct 7, 2024
4d9f8b6
remove # from products
oschwengers Oct 7, 2024
ae4142b
remove suspect first character
oschwengers Oct 7, 2024
51f4d11
remove remnant of terms
oschwengers Oct 10, 2024
cb8815c
discrad pure tmRNA CDS product descriptions
oschwengers Oct 10, 2024
be07551
Merge branch 'main' into fix-cds-products
oschwengers Oct 10, 2024
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28 changes: 26 additions & 2 deletions bakta/features/annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,12 @@
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_DOMAIN_CONTAINING = re.compile(r'domain-containing protein', flags=re.IGNORECASE)
RE_PROTEIN_REMNANT = re.compile(r'Remnant of ', re.IGNORECASE)
RE_PROTEIN_TMRNA = re.compile(r'TmRNA', flags=re.IGNORECASE)
RE_PROTEIN_NO_LETTERS = re.compile(r'[^A-Za-z]')
RE_PROTEIN_SUSPECT_CHARS = re.compile(r'[.@=?%]')
RE_PROTEIN_SUSPECT_CHARS_DISCARD = re.compile(r'[.#]')
RE_PROTEIN_SUSPECT_CHARS_REPLACE = re.compile(r'[@=?%]')
RE_PROTEIN_SUSPECT_CHARS_BEGINNING = '_\-+.:,;/\\\''
RE_PROTEIN_PERIOD_SEPARATOR = re.compile(r'([a-zA-Z0-9]+)\.([a-zA-Z0-9]+)')
RE_PROTEIN_WRONG_PRIMES = re.compile(r'[\u2032\u0060\u00B4]') # prime (′), grave accent (`), acute accent (´)
RE_PROTEIN_WEIGHT = re.compile(r' [0-9]+(?:\.[0-9]+)? k?da ', flags=re.IGNORECASE)
Expand Down Expand Up @@ -536,9 +540,19 @@ def revise_cds_product(product: str):
product = re.sub(RE_PROTEIN_PERIOD_SEPARATOR, r'\1-\2', product) # replace separator periods
if(product != old_product):
log.info('fix product: replace separator periods. new=%s, old=%s', product, old_product)

old_product = product
if(product[0] in RE_PROTEIN_SUSPECT_CHARS_BEGINNING): # remove suspect first character
product = product[1:]
log.info('fix product: replace invalid first character. new=%s, old=%s', product, old_product)

old_product = product
product = RE_PROTEIN_SUSPECT_CHARS_DISCARD.sub('', product) # remove suspect characters
if(product != old_product):
log.info('fix product: replace invalid characters. new=%s, old=%s', product, old_product)

old_product = product
product = RE_PROTEIN_SUSPECT_CHARS.sub('', product) # remove suspect characters
product = RE_PROTEIN_SUSPECT_CHARS_REPLACE.sub(' ', product) # replace suspect characters by single whitespace
if(product != old_product):
log.info('fix product: replace invalid characters. new=%s, old=%s', product, old_product)

Expand All @@ -552,6 +566,11 @@ def revise_cds_product(product: str):
if(product != old_product):
log.info('fix product: replace FOG ids. new=%s, old=%s', product, old_product)

old_product = product
product = RE_PROTEIN_REMNANT.sub('', product) # remove 'Remnant of's
if(product != old_product):
log.info('fix product: replace remnant ofs. new=%s, old=%s', product, old_product)

old_product = product
dufs = [] # replace DUF-containing products
for m in RE_DOMAIN_OF_UNKNOWN_FUNCTION.finditer(product):
Expand Down Expand Up @@ -593,6 +612,11 @@ def revise_cds_product(product: str):
product = product.replace('_', '-')
if(product != old_product):
log.info('fix product: replace domain name underscores. new=%s, old=%s', product, old_product)

old_product = product
if(RE_PROTEIN_TMRNA.fullmatch(product)):
product = ''
log.info('fix product: discard pure tmRNA product descriptions. new=%s, old=%s', product, old_product)

old_product = product
if(
Expand Down
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