#Alignments and output data
unaligned_DNA = LoadSeqs(data=curated_protein_list,
moltype=DNA,
aligned=False)
unaligned_AA = unaligned_DNA.getTranslation()
#Generate alignments using muscle
aligned_AA = mafft_align_unaligned_seqs(unaligned_AA, PROTEIN)
#Replace the aminoacid sequences with the nucleotide sequence
aligned_DNA = aligned_AA.replaceSeqs(unaligned_DNA)
#Make protein trees using FastTree
protein_tree = build_tree_fasttree(aligned_AA, PROTEIN)
protein_tree_output = open(
protein_tree_folder + "/" + cluster + ".tre", 'w')
protein_tree_output.write(protein_tree.getNewick(with_distances=True))
protein_tree_output.close()
#Make nucleotide trees using FastTree
nucleotide_tree = build_tree_fasttree(aligned_DNA, DNA)
nucleotide_tree_output = open(dna_tree_folder + "/" + cluster + ".tre",
'w')
nucleotide_tree_output.write(
nucleotide_tree.getNewick(with_distances=True))
nucleotide_tree_output.close()
#Write the unaligned and aligned sequences
unaligned_DNA.writeToFile(dna_unaligned_folder + "/" + cluster +
continue
#Alignments and output data
unaligned_DNA = LoadSeqs(data=curated_protein_list, moltype=DNA, aligned=False)
unaligned_AA = unaligned_DNA.getTranslation()
#Generate alignments using muscle
aligned_AA = mafft_align_unaligned_seqs(unaligned_AA, PROTEIN)
#Replace the aminoacid sequences with the nucleotide sequence
aligned_DNA = aligned_AA.replaceSeqs(unaligned_DNA)
#Make protein trees using FastTree
protein_tree = build_tree_fasttree(aligned_AA, PROTEIN)
#Tree file
tree_output = open(tree_folder + "/" + cluster + ".tre", 'w')
tree_output.write(protein_tree.getNewick(with_distances=True))
#Write the unaligned and aligned sequences
unaligned_DNA.writeToFile(dna_unaligned_folder + "/" + cluster + ".fna", format="fasta")
unaligned_AA.writeToFile(protein_unaligned_folder + "/" + cluster + ".faa", format="fasta")
aligned_DNA.writeToFile(dna_aligned_folder + "/" + cluster + ".fna", format="fasta")
aligned_AA.writeToFile(protein_alignment_folder + "/" + cluster + ".faa", format="fasta")
tree_output.close()
#Print log files
#Alignments and output data
unaligned_DNA = LoadSeqs(data=curated_protein_list,
moltype=DNA,
aligned=False)
unaligned_AA = unaligned_DNA.getTranslation()
#Generate alignments using muscle
aligned_AA = mafft_align_unaligned_seqs(unaligned_AA, PROTEIN)
#Replace the aminoacid sequences with the nucleotide sequence
aligned_DNA = aligned_AA.replaceSeqs(unaligned_DNA)
#Make protein trees using FastTree
protein_tree = build_tree_fasttree(aligned_AA, PROTEIN)
#Tree file
tree_output = open(tree_folder + "/" + cluster + ".tre", 'w')
tree_output.write(protein_tree.getNewick(with_distances=True))
#Write the unaligned and aligned sequences
unaligned_DNA.writeToFile(dna_unaligned_folder + "/" + cluster +
".fna",
format="fasta")
unaligned_AA.writeToFile(protein_unaligned_folder + "/" + cluster +
".faa",
format="fasta")
aligned_DNA.writeToFile(dna_aligned_folder + "/" + cluster + ".fna",
format="fasta")
continue
#Alignments and output data
unaligned_DNA = LoadSeqs(data=curated_protein_list, moltype=DNA, aligned=False)
unaligned_AA = unaligned_DNA.getTranslation()
#Generate alignments using muscle
aligned_AA = mafft_align_unaligned_seqs(unaligned_AA, PROTEIN)
#Replace the aminoacid sequences with the nucleotide sequence
aligned_DNA = aligned_AA.replaceSeqs(unaligned_DNA)
#Make protein trees using FastTree
protein_tree = build_tree_fasttree(aligned_AA, PROTEIN)
protein_tree_output = open(protein_tree_folder + "/" + cluster + ".tre", 'w')
protein_tree_output.write(protein_tree.getNewick(with_distances=True))
protein_tree_output.close()
#Make nucleotide trees using FastTree
nucleotide_tree = build_tree_fasttree(aligned_DNA, DNA)
nucleotide_tree_output = open(dna_tree_folder + "/" + cluster + ".tre", 'w')
nucleotide_tree_output.write(nucleotide_tree.getNewick(with_distances=True))
nucleotide_tree_output.close()
#Write the unaligned and aligned sequences
unaligned_DNA.writeToFile(dna_unaligned_folder + "/" + cluster + ".fna", format="fasta")
unaligned_AA.writeToFile(protein_unaligned_folder + "/" + cluster + ".faa", format="fasta")
aligned_DNA.writeToFile(dna_aligned_folder + "/" + cluster + ".fna", format="fasta")
