Sequence types

Simple types

SeqAn simple types represent alphabets for DNA, RNA and amino acids.

>>> print seqan.DNA('A')
A
>>> print seqan.RNA('U')
U
>>> print seqan.IUPAC('V')
V
>>> print seqan.AminoAcid('K')
K

The DNA and RNA types have versions that can represent ambiguous characters.

>>> print seqan.DNA5('N')
N
>>> print seqan.DNA.valueSize
4
>>> print seqan.DNA5.valueSize
5
>>> print seqan.RNA5('N')
N

Strings

Strings are sequence containers.

>>> seq = seqan.StringDNA5('ACGTNNNNACGT')
>>> print seq[4:8]
NNNN
>>> seq = seqan.StringDNA('ACGTACGTACGT')
>>> print seq[4:8]
ACGT
>>> print seqan.StringDNA('AAGG').reversecomplement()
CCTT

String sets

A StringSet is a container of strings.

>>> seqs = seqan.StringDNASet(('ACGT', 'AAAA', 'GGGG'))
>>> print type(seqs[0]).__name__
StringDNA
>>> print seqs[0]
ACGT
>>> print seqs[1]
AAAA
>>> print seqs[2]
GGGG

Input/output

Sequences can be read into string sets from FASTA files:

>>> num_bases_read, seqs, seq_ids = seqan.readFastaDNA5('my-fasta-file.fa')
>>> print 'Read %d bases in %d sequences' % (num_bases_read, len(seqs))
Read 3412 bases in 10 sequences