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from __future__ import print_function
import os

import dendropy


    

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from Bio.Align.Applications import MafftCommandline
mafft_cline = MafftCommandline(input='sample.fasta', ep=0.123, reorder=True, maxiterate=1000, localpair=True)
print(mafft_cline)
stdout, stderr = mafft_cline()
with open('align.fasta', 'w') as w:
    w.write(stdout)


    

    




mafft --localpair --maxiterate 1000 --ep 0.123 --reorder sample.fasta

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os.system('trimal -automated1 -in align.fasta -out trim.fasta -fasta')


    

    
Out[6]:





0

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from Bio.Align.Applications import MuscleCommandline

my_genes = ['NP', 'L', 'VP35', 'VP40']

for gene in my_genes:
    muscle_cline = MuscleCommandline(input='%s_P.fasta' % gene)
    print(muscle_cline)
    stdout, stderr = muscle_cline()
    with open('%s_P_align.fasta' % gene, 'w') as w:
        w.write(stdout)


    

    




muscle -in NP_P.fasta
muscle -in L_P.fasta
muscle -in VP35_P.fasta
muscle -in VP40_P.fasta

In [8]:

    

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_protein

for gene in my_genes:
    gene_seqs = {}
    unal_gene = SeqIO.parse('%s.fasta' % gene, 'fasta')
    for rec in unal_gene:
        gene_seqs[rec.id] = rec.seq

    al_prot = SeqIO.parse('%s_P_align.fasta' % gene, 'fasta')
    al_genes = []
    for protein in al_prot:
        my_id = protein.id
        seq = ''
        pos = 0
        for c in protein.seq:
            if c == '-':
                seq += '---'
            else:
                seq += str(gene_seqs[my_id][pos:pos + 3])
                pos += 3
        al_genes.append(SeqRecord(Seq(seq), id=my_id))


    SeqIO.write(al_genes, '%s_align.fasta' % gene, 'fasta')


    

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