Biology

class polars_extensions.biology.BioExtensionNamespace(expr: Expr)

Bases: object

Polars expression namespace for biological sequence conversions and analysis.

Methods

at_content()	Return AT content as a percentage.
contains_motif(motif)	Return True if sequence contains the given motif.
count_codons()	Return the number of codons (sequence length / 3).
count_motif(motif)	Count occurrences of a motif in the sequence.
count_nucleotides()	Return a struct of counts for A, T, G, and C.
delete_sequence(start, end)	Delete a segment of the sequence from start to end.
dna_complement()	Return the DNA complement (A↔T, C↔G).
dna_reverse_complement()	Return the reverse complement of DNA sequence.
dna_to_rna()	Convert DNA sequences (A, T, G, C) to RNA sequences (A, U, G, C).
dna_transcribe()	Transcribe DNA to RNA (same as dna_to_rna).
gc_content()	Return GC content as a percentage.
gc_skew()	Compute GC skew = (G - C) / (G + C).
hamming_distance(other)	Return Hamming distance between two equal-length sequences.
insert_sequence(position, subseq)	Insert a subsequence at the given position.
is_valid_dna()	Return True if the sequence only contains valid DNA bases (A, T, G, C, N).
is_valid_rna()	Return True if the sequence only contains valid RNA bases (A, U, G, C, N).
mutate_sequence(position, new_base)	Mutate a sequence by replacing one base at a given position (0-indexed).
repeat_sequence(n)	Repeat the sequence n times.
reverse_sequence()	Reverse a sequence string.
rna_to_dna()	Convert RNA sequences (A, U, G, C) to DNA sequences (A, T, G, C).
sequence_length()	Return the sequence length.

at_content() → Expr

Return AT content as a percentage.

contains_motif(motif: str) → Expr

Return True if sequence contains the given motif.

count_codons() → Expr

Return the number of codons (sequence length / 3).

count_motif(motif: str) → Expr

Count occurrences of a motif in the sequence.

count_nucleotides() → Expr

Return a struct of counts for A, T, G, and C.

delete_sequence(start: int, end: int) → Expr

Delete a segment of the sequence from start to end.

dna_complement() → Expr

Return the DNA complement (A↔T, C↔G).

dna_reverse_complement() → Expr

Return the reverse complement of DNA sequence.

dna_to_rna() → Expr

Convert DNA sequences (A, T, G, C) to RNA sequences (A, U, G, C).

dna_transcribe() → Expr

Transcribe DNA to RNA (same as dna_to_rna).

gc_content() → Expr

Return GC content as a percentage.

gc_skew() → Expr

Compute GC skew = (G - C) / (G + C).

hamming_distance(

other: Expr,

) → Expr

Return Hamming distance between two equal-length sequences.

Parameters:

otherpl.Expr

Another expression containing sequences of equal length.

insert_sequence(

position: int,

subseq: str,

) → Expr

Insert a subsequence at the given position.

is_valid_dna() → Expr

Return True if the sequence only contains valid DNA bases (A, T, G, C, N).

is_valid_rna() → Expr

Return True if the sequence only contains valid RNA bases (A, U, G, C, N).

mutate_sequence(

position: int,

new_base: str,

) → Expr

Mutate a sequence by replacing one base at a given position (0-indexed).

repeat_sequence(n: int) → Expr

Repeat the sequence n times.

reverse_sequence() → Expr

Reverse a sequence string.

rna_to_dna() → Expr

Convert RNA sequences (A, U, G, C) to DNA sequences (A, T, G, C).

sequence_length() → Expr

Return the sequence length.