bio.builtin
¶
Source code: bio/builtin.seq
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bio.builtin.
seqs
(x)¶ Returns an iterator over sequences from the specified object by invoking the __seqs__ magic method.
__seqs__ is defined for most common formats, like FASTA, FASTQ, SAM and BAM.
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bio.builtin.
split
(self: seq, k: int, step: int)¶ Iterator over length-k subsequences of the given sequence with the specified step size.
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bio.builtin.
kmers
[K]
(self: seq, step: int)¶ Iterator over k-mers (type K) of the given sequence with the specified step size. Note that k-mers spanning ambiguous bases will be skipped.
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bio.builtin.
kmers_with_pos
[K]
(self: seq, step: int)¶ Iterator over (0-based index, k-mer) tuples of the given sequence with the specified step size. Note that k-mers spanning ambiguous bases will be skipped.
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bio.builtin.
revcomp
(s)¶ Returns the reverse complement of the argument sequence or k-mer.
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bio.builtin.
revcomp_with_pos
(t)¶ Returns the reverse complement of the argument sequence or k-mer, where the argument also contains a position (e.g. as yielded by kmers_with_pos).
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bio.builtin.
canonical
(k)¶ Returns the minimum of a sequence / k-mer and its reverse complement.
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bio.builtin.
canonical_with_pos
(t)¶ Returns the minimum of a sequence / k-mer and its reverse complement, where the argument also contains a position (e.g. as yielded by kmers_with_pos).
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bio.builtin.
base
[K, T]
(kmer: K, idx: int, b: T)¶ Returns a new k-mer based on kmer with the base at idx replaced with b.