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search.py
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import re
"""
This file contains the search functions that moclass uses
The big blocks of text are for convenient testing of the regular expressions,
Copy the regex and the block of text to a website like https://regex101.com/ so you can play around with it
"""
TRANSCRIPT_RE = "(?P<transcript>NM_?[0-9]+)"
# http://www.hgvs.org/mutnomen/examplesDNA.html
# https://regex101.com/r/47zMoc/1
"""
c.-12G>A
c.1A>C
c.23G>C
c.88+2T>G
c.89-1G>T
c.123+89C>T
c.329G>C
c.*70T>A
c.*293C>A
c.13del
c.13delG
c.4del
c.4delG
c.301-3del
c.301-3delT
c.-11_-4del
c.92_94del
c.92_94delGAC
c.*8_*21del
c.120_123+48del
c.124-12_129del
c.7_8del
c.7_8delTG
c.123del
c.123delA
c.13-?_300+?del
c.(?_-30)_(*220_?)del
c.13-23_301-143del
c.13dup
c.13dupG
c.92_94dup
c.92_94dupGAC
c.120_123+48dup
c.7_8dup
c.7_8dupTG
c.51_52insT
c.51_52insGAGA
c.123+54_123+55insAB012345.1
c.*70_71[6]
c.*70CA[6]
c.*70_71[8]
c.*70CA[8]
c.*70_71[6];[11]
c.*70CA[6];[11]
c.77_80inv
c.77_80invCTGA
c.1670_1673inv
c.1023_1024delinsAT
c.1670_1673delinsTTCC
c.1458_1459delCCinsTT
"""
C_DOT_RE_LIST = [re.compile(regex, re.IGNORECASE) for regex in [
# all?
"(?P<cdot>c[.](?P<cdot_pos>[-*]?[0-9]+(?P<cdot_pos2>[-+_*]+[0-9?]+)?(?P<cdot_pos3>[-+_*]+[0-9]+)?(?P<cdot_pos4>[-+_*]+[0-9?]+)?)(?P<cdot_ref>[actg]+)?(?P<cdot_type>dup|delins|del|ins|>|>|inv)(?P<cdot_alt>[actg]+)?(ins(?P<cdot_ins>[actg]+))?)",
# sub
# "(?P<cdot>c[.])(?P<cdot_pos>[-*]?[0-9]+(?P<cdot_pos2>[-+_][0-9]+)?)(?P<cdot_ref>[acgt]+)([>]|>)(?P<cdot_alt>[actg]+)",
# del
# "(?P<cdot>c[.])(?P<cdot_pos>[-*]?[0-9]+(?P<cdot_pos2>[-+_*]+[0-9?]+)?(?P<cdot_pos3>[-+_*]+[0-9]+)?(?P<cdot_pos4>[-+_*]+[0-9?]+)?)del(?P<cdot_ref>[actg]+)?",
# dup
# "(?P<cdot>c[.])(?P<cdot_pos>[-*]?[0-9]+(?P<cdot_pos2>[-+_*]+[0-9?]+)?(?P<cdot_pos3>[-+_*]+[0-9]+)?(?P<cdot_pos4>[-+_*]+[0-9?]+)?)dup(?P<cdot_ref>[actg]+)?",
# ins
# "",
# repeat
"(?P<cdot>c[.](?P<cdot_pos>[-*]?[0-9]+(?P<cdot_pos2>[-+_][0-9]+)?)(?P<cdot_ref>[actg]+)?\[(?P<cdot_repeats>[0-9]+)\](;\[(?P<cdot_repeats2>[0-9]+)\])?)"
]]
# https://www.hgmd.cf.ac.uk/docs/cd_amino.html
# https://regex101.com/r/rMLj6y/1
"""
p.Trp24Cys
p.(Trp24Cys)
p.Trp24Ter
p.Trp24*
p.Cys188=
p.Met1?
p.Gln2366Lys
p.Trp26Cys
p.Trp26Ter
p.Trp26*
p.Trp26_Leu833del
p.Leu2_Met124del
p.Met1_Leu2insArgSerThrVal
p.Met1ext-5
p.(Gly56Ala^Ser^Cys)
p.Trp24_Val25delinsCysArg
p.?
p.0
p.0?
"""
P_DOT_RE_LIST = [re.compile(regex, re.IGNORECASE) for regex in [
# missense, nonsense and silent
"(?P<pdot>p[.](?P<pdot_from>[a-z*]+)(?P<pdot_pos>[0-9]+)(?P<pdot_to>[a-z*=?]+))",
# predicted missense, nonsense and silent
"(?P<pdot>p[.]\((?P<pdot_from>[a-z*]+)(?P<pdot_pos>[0-9]+)(?P<pdot_to>[a-z*=?]+)\))",
# del
"(?P<pdot>p[.](?P<pdot_from>(?P<pdot_del_from>[a-z*]+)(?P<pdot_del_from_pos>[0-9]+)_(?P<pdot_del_to>[a-z]+)(?P<pdot_del_to_pos>[0-9]+))del)",
# dup
"(?P<pdot>p[.](?P<pdot_from>(?P<pdot_dup_from>[a-z*]+)(?P<pdot_dup_from_pos>[0-9]+)_(?P<pdot_dup_to>[a-z]+)(?P<pdot_dup_to_pos>[0-9]+))dup)",
# ins
"(?P<pdot>p[.](?P<pdot_from>(?P<pdot_del_from>[a-z*]+)(?P<pdot_del_from_pos>[0-9]+)_(?P<pdot_del_to>[a-z]+)(?P<pdot_del_to_pos>[0-9]+))ins(?P<pdot_to>[^\d\s^)_]+))",
# delins
"(?P<pdot>p[.](?P<pdot_from>(?P<pdot_del_from>[a-z*]+)(?P<pdot_del_from_pos>[0-9]+)_(?P<pdot_del_to>[a-z]+)(?P<pdot_del_to_pos>[0-9]+))delins(?P<pdot_to>[^\d\s^)_]+))",
# no protein produced, unkown effect and splicing
"p\.(0|0\?|\?|\(=\)|=)",
]]
TRANSCRIPT_STR = "(?P<transcript>NM_?(?P<transcript_number>[0-9]+)(?P<transcript_version>[.][0-9]+)?)"
TRANSCRIPT_RE = re.compile(TRANSCRIPT_STR, re.IGNORECASE)
# gene regex for gene:cdot search
GENE_CDOT_STR = "\s*(?P<gene>[^:]+)"
CHR_POS_END_REF_ALT_STR = "(?P<chr>(chr)?[0-9]+)[\s:_-]+(?P<pos>[0-9]+)[\s:_-]+(?P<end>[0-9]+)?(?P<ref>[actg]+)[\s:_-]+(?P<alt>[actg]+)"
CHR_POS_END_REF_ALT_RE = re.compile(CHR_POS_END_REF_ALT_STR, re.IGNORECASE)
RS_RE = re.compile("(?P<rs>rs[0-9]+)", re.IGNORECASE)
def parse_rs(search) -> dict:
"""
Look for an rs#, for example: rs121913279
"""
result = {}
if m := RS_RE.search(search):
result.update(m.groupdict())
return result
def parse_transcript(search) -> dict:
"""
Look for a transcript, for example: NM_001042492.3
"""
result = {}
if m := TRANSCRIPT_RE.search(search):
result.update(m.groupdict())
return result
def parse_cdot(search) -> dict:
"""
Look far a cdot, for example: c.23G>C
"""
result = {}
for regex in C_DOT_RE_LIST:
if m := regex.search(search):
result.update(m.groupdict())
return result
def parse_gene_cdot(search) -> dict:
"""
Look for a gene:cdot, for example: NF1:c.5349T>A
"""
result = {}
for regex in C_DOT_RE_LIST:
cdot = regex.pattern
pattern = f"{GENE_CDOT_STR}:{cdot}"
if m := re.search(pattern, search, re.IGNORECASE):
m = m.groupdict()
# m["gene_cdot"] = m["cdot"]
# del m["cdot"]
result.update(m)
return result
def parse_pdot(search) -> dict:
"""
Look for a pdot, for example: p.Trp24Ter
"""
result = {}
for regex in P_DOT_RE_LIST:
if m := regex.search(search):
result.update(m.groupdict())
return result
def parse_pos(search):
"""
Look for a 'chr start end ref alt' text, for example: chr3 12345 12345 A C
"""
result = {}
if m := CHR_POS_END_REF_ALT_RE.search(search):
result.update(m.groupdict())
return result
def parse_search(search) -> dict:
"""
The main search parsing function, it calls all the other functions
and just adds all the metadata that is identified together
"""
# Ignore exon+number and strip whitespaces
search = re.sub(r'exon.*(?=:)', '', search).replace(" ", "")
result = parse_rs(search)
transcript = parse_transcript(search)
if transcript:
result.update(transcript)
result.update(parse_cdot(search))
else: # gene:cdot check
try:
result.update(parse_gene_cdot(search))
# rename cdot to gene_cdot
# so there is a diff between transcript:cdot and gene:cdot
result["gene_cdot"] = result["cdot"]
del result["cdot"]
except Exception as e:
print(f"Invalid or missing result: {e}")
if "cdot_ref" in result:
result["ref"] = result["cdot_ref"]
if "cdot_alt" in result:
result["alt"] = result["cdot_alt"]
result.update(parse_pdot(search))
result.update(parse_pos(search))
return result