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.. _alignment-controllers:
Using alignment application controllers to align unaligned sequences
====================================================================
.. sectionauthor:: Daniel McDonald
This document provides examples of how to align sequences using the alignment application controllers. Each alignment application controller module provides the support method ``align_unaligned_seqs``. This method takes as input a ``SequenceCollection`` object or a dict mapping sequence ids to sequences, the ``MolType`` of the sequences, and an option dict containing specific parameter settings. As output, the method returns an ``Alignment`` object.
First, lets import all of the ``align_unaligned_seqs`` methods:
.. doctest::
>>> from cogent.app.clustalw import align_unaligned_seqs as clustalw_align_unaligned_seqs
>>> from cogent.app.muscle import align_unaligned_seqs as muscle_align_unaligned_seqs
>>> from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
Next, we'll load our test data. We will be using DNA sequences for this example:
.. doctest::
>>> from cogent.core.moltype import DNA
>>> from cogent import LoadSeqs
>>> unaligned_seqs = LoadSeqs(filename='data/test2.fasta', aligned=False)
Lets align some sequences using default parameters!
.. note:: Output is truncated for document formatting
.. doctest::
>>> clustalw_aln = clustalw_align_unaligned_seqs(unaligned_seqs, DNA)
>>> muscle_aln = muscle_align_unaligned_seqs(unaligned_seqs, DNA)
>>> mafft_aln = mafft_align_unaligned_seqs(unaligned_seqs, DNA)
>>> clustalw_aln
5 x 60 dna alignment: NineBande[------CGCCA...], Mouse[GCAGTGAGCCA...], ...
>>> muscle_aln
5 x 60 dna alignment: NineBande[------CGCCA...], Mouse[GCAGTGAGCCA...], ...
>>> mafft_aln
5 x 60 dna alignment: NineBande[------CGCCA...], Mouse[GCAGTGAGCCA...], ...
To change specific parameters, simply specify the parameters in a dict and pass it in:
.. note:: Output is truncated for document formatting
.. doctest::
>>> clustalw_params = {'-gapopen':-3, '-quicktree':True}
>>> clustalw_aln = clustalw_align_unaligned_seqs(unaligned_seqs, DNA, params=clustalw_params)
>>> clustalw_aln
5 x 60 dna alignment: NineBande[------CGCCA...], Mouse[GCAGTGAGCCA...], ...
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