Name: Python Bio Regular Expressions
Author: Pavel-Kravchenko

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Python Bio Regular Expressions | Skills Pool

import re

# Stop codons
stop = re.compile(r'TAA|TAG|TGA')

# Overlapping ATG starts — requires lookahead
for m in re.finditer(r'(?=(ATG))', dna):
    print(m.start(), m.group(1))

# ORF: greedy (longest) vs lazy (shortest)
greedy = re.findall(r'ATG.*TAG', dna)    # first ATG to LAST TAG
lazy   = re.findall(r'ATG.*?TAG', dna)  # first ATG to nearest TAG

# Homopolymer runs (4+ bases)
for m in re.finditer(r'(.)\1{3,}', dna):
    print(m.group(), m.start(), len(m.group()))

# Tandem repeats
for m in re.finditer(r'([ATGC]{3})\1+', dna):
    unit = m.group(1)
    copies = len(m.group()) // len(unit)

# IUPAC ambiguity: translate before matching
IUPAC = {'N':'[ATGC]','R':'[AG]','Y':'[CT]','W':'[AT]','S':'[GC]',
         'M':'[AC]','K':'[GT]','B':'[CGT]','D':'[AGT]','H':'[ACT]','V':'[ACG]'}
def iupac_to_regex(seq):
    return ''.join(IUPAC.get(b, b) for b in seq.upper())

# Restriction digest (overlapping sites)
def find_cut_positions(dna, site, cut_offset):
    return [m.start() + cut_offset for m in re.finditer(f'(?={site})', dna.upper())]

# FASTA header parsing (named groups)
header = ">sp|P04637|P53_HUMAN Cellular tumor antigen OS=Homo sapiens"
pat = r'>sp\|(?P<acc>[^|]+)\|(?P<entry>\S+)\s+(?P<desc>.+?)\s+OS=(?P<org>.+)'
m = re.search(pat, header)
# m.group('acc'), m.group('org') etc.

# Transcription: T→U
rna = re.sub('T', 'U', dna)

# Split at restriction sites
fragments = re.split(r'GAATTC|GGATCC|AAGCTT', dna)

# Multi-line FASTA headers
headers = re.findall(r'^>.*', fasta, re.MULTILINE)

# Non-standard nucleotides
non_std = re.findall(r'[^ATGCN]', seq)

# Mask homopolymers with N
def mask_repeat(m):
    return 'N' * len(m.group()) if len(m.group()) >= 5 else m.group()
masked = re.sub(r'(.)\1{2,}', mask_repeat, dna)

Syntax	Meaning	Bio use
`(?=pat)`	Positive lookahead	Overlapping matches; ATG not consuming
`(?!pat)`	Negative lookahead	ATG not followed by stop
`(?<=pat)`	Positive lookbehind	Bases after restriction site
`(?<!pat)`	Negative lookbehind	Context-excluded matches

Function	Returns	Use
`re.search(pat, s)`	First match object or None	Check if pattern exists
`re.findall(pat, s)`	List of strings (or tuples with groups)	All non-overlapping matches
`re.finditer(pat, s)`	Iterator of match objects	All matches with positions
`re.sub(pat, repl, s)`	Modified string	Replace matches
`re.split(pat, s)`	List of strings	Split on pattern
`re.compile(pat)`	Compiled regex	Reuse expensive patterns

Function	Returns	Use
`re.search(pat, s)`	First match object or None	Check if pattern exists
`re.findall(pat, s)`	List of strings (or tuples with groups)	All non-overlapping matches
`re.finditer(pat, s)`	Iterator of match objects	All matches with positions
`re.sub(pat, repl, s)`	Modified string	Replace matches
`re.split(pat, s)`	List of strings	Split on pattern
`re.compile(pat)`	Compiled regex	Reuse expensive patterns

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