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 cogent import LoadSeqs, DNA
>>> aln = LoadSeqs("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
>NineBande
AAACTGCTGTTCTCATGCTGTAATAAGTTGGCATGAGTATTTGTGCCACA
>Mouse
AAACTGCTGGTCTCAGGCTGTAATGAGCTGGCATGAGCATCTGTGCCACA
>Human
AAACTGCTGTTCTCATGCTGTAATGAGCTGGCATGAGTATTTGTGCCACA
>HowlerMon
AAACTGCTGTTCTCATGCTGTAATGAGCTGGCATGAGTATTTGTGCCACA
>DogFaced
AAACTGCTGTTCTCATGCTGTAATGAGTTGGCATGAGTATTTGTGCCACA