Getting the reverse complementΒΆ
Section author: Gavin Huttley
This is a property of DNA, and hence alignments need to be created with the appropriate MolType
. In the following example, the alignment is truncated to just 50 bases for the sake of simplifying the presentation.
>>> from cogent3 import load_aligned_seqs
>>> aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna")[:50]
The original alignment looks like this.
>>> print(aln)
>Human
TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGCAGTTT
>HowlerMon
TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGCAGTTT
>Mouse
TGTGGCACAGATGCTCATGCCAGCTCATTACAGCCTGAGACCAGCAGTTT
>NineBande
TGTGGCACAAATACTCATGCCAACTTATTACAGCATGAGAACAGCAGTTT
>DogFaced
TGTGGCACAAATACTCATGCCAACTCATTACAGCATGAGAACAGCAGTTT
We do reverse complement very simply.
>>> naln = aln.rc()
The reverse complemented alignment looks like this.
>>> print(naln)
>Human
AAACTGCTGTTCTCATGCTGTAATGAGCTGGCATGAGTATTTGTGCCACA
>HowlerMon
AAACTGCTGTTCTCATGCTGTAATGAGCTGGCATGAGTATTTGTGCCACA
>Mouse
AAACTGCTGGTCTCAGGCTGTAATGAGCTGGCATGAGCATCTGTGCCACA
>NineBande
AAACTGCTGTTCTCATGCTGTAATAAGTTGGCATGAGTATTTGTGCCACA
>DogFaced
AAACTGCTGTTCTCATGCTGTAATGAGTTGGCATGAGTATTTGTGCCACA