create alignment in Biopython without input file

Question

I have an alignment of protein sequences in a dictionary (id_prot as key and aligned sequence as value; could be another format), and I would like to use this alignment to build a NJ tree with Biopython

However, according to the documentation, the only way to load sequences to be used for phylogenetic analyses is from an input file. For instance:

aln = AlignIO.read('Tests/TreeConstruction/msa.phy', 'phylip')

Does anyone know how to load sequences in the aln variable without reading an input file ?

Go back a step or two- how did your alignment get read into a dictionary in the first place? — Chris_Rands, Sep 10 '19 at 08:29
Your custom script could output a standard alignment format, then you've solved your problem — Chris_Rands, Sep 11 '19 at 09:48
as stated below, I have hundred of thousands of alignments ... I would like to keep everything within python with no output file. Otherwise I could also use a standard NJ program instead of Biopython. — Romain, Sep 11 '19 at 10:09

BioGeek · Answer 1 · 2019-09-01T09:52:28.310

Create the required input in Phylip format from your dictionary and load it with StringIO. Note that the The sequence/protein ID can be up to 10 characters long. IDs less than 10 characters must have spaces appended to them to reach the 10 character fixed width.

from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
from Bio import AlignIO
from io import StringIO

dct = {'Alpha':   'AACGTGGCCACAT',
       'Beta':    'AAGGTCGCCACAC',
       'Gamma':   'CAGTTCGCCACAA',
       'Delta':   'GAGATTTCCGCCT',
       'Epsilon': 'GAGATCTCCGCCC'}


count = len(dct)
length = max(map(len, dct.values()))

msa = f" {count} {length}\n"
msa += '\n'.join(f"{prot_id:<10} {sequence}" for prot_id, sequence in dct.items())
print(msa)
print()

aln = AlignIO.read(StringIO(msa), 'phylip')
print(aln)
print()

calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
print(dm)
print()

constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(aln)
print(tree)

Output:

 5 13
Alpha      AACGTGGCCACAT
Beta       AAGGTCGCCACAC
Gamma      CAGTTCGCCACAA
Delta      GAGATTTCCGCCT
Epsilon    GAGATCTCCGCCC

SingleLetterAlphabet() alignment with 5 rows and 13 columns
AACGTGGCCACAT Alpha
AAGGTCGCCACAC Beta
CAGTTCGCCACAA Gamma
GAGATTTCCGCCT Delta
GAGATCTCCGCCC Epsilon

Alpha   0
Beta    0.23076923076923073 0
Gamma   0.3846153846153846  0.23076923076923073 0
Delta   0.5384615384615384  0.5384615384615384  0.5384615384615384  0
Epsilon 0.6153846153846154  0.3846153846153846  0.46153846153846156 0.15384615384615385 0
    Alpha   Beta    Gamma   Delta   Epsilon

Tree(rooted=False)
    Clade(branch_length=0, name='Inner3')
        Clade(branch_length=0.18269230769230765, name='Alpha')
        Clade(branch_length=0.04807692307692307, name='Beta')
        Clade(branch_length=0.04807692307692307, name='Inner2')
            Clade(branch_length=0.27884615384615385, name='Inner1')
                Clade(branch_length=0.051282051282051266, name='Epsilon')
                Clade(branch_length=0.10256410256410259, name='Delta')
            Clade(branch_length=0.14423076923076922, name='Gamma')

Many thanks for your reply. However, since I want to do it for hundred of thousands of times, I would like to not use an input file (to avoid I/O limitations). — Romain, Sep 02 '19 at 07:08

create alignment in Biopython without input file

1 Answers1