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Getting the reverse complement
==============================
.. sectionauthor:: 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.
.. doctest::
>>> from cogent import LoadSeqs, DNA
>>> aln = LoadSeqs("data/long_testseqs.fasta", moltype=DNA)[:50]
The original alignment looks like this.
.. doctest::
>>> print aln
>Human
TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGCAGTTT
>HowlerMon
TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGCAGTTT
>Mouse
TGTGGCACAGATGCTCATGCCAGCTCATTACAGCCTGAGACCAGCAGTTT
>NineBande
TGTGGCACAAATACTCATGCCAACTTATTACAGCATGAGAACAGCAGTTT
>DogFaced
TGTGGCACAAATACTCATGCCAACTCATTACAGCATGAGAACAGCAGTTT
<BLANKLINE>
We do reverse complement very simply.
.. doctest::
>>> naln = aln.rc()
The reverse complemented alignment looks like this.
.. doctest::
>>> print naln
>NineBande
AAACTGCTGTTCTCATGCTGTAATAAGTTGGCATGAGTATTTGTGCCACA
>Mouse
AAACTGCTGGTCTCAGGCTGTAATGAGCTGGCATGAGCATCTGTGCCACA
>Human
AAACTGCTGTTCTCATGCTGTAATGAGCTGGCATGAGTATTTGTGCCACA
>HowlerMon
AAACTGCTGTTCTCATGCTGTAATGAGCTGGCATGAGTATTTGTGCCACA
>DogFaced
AAACTGCTGTTCTCATGCTGTAATGAGTTGGCATGAGTATTTGTGCCACA
<BLANKLINE>
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