else:
frameshift_cases.append([cluster, genome_id, protein_id])
if len(curated_protein_list) < 2: # Only take those clusters with 3 sequences or more
clusters_too_short.append(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)
#Output files
aligned_dna_file = dna_aligned_folder + "/" + cluster + ".fna"
aligned_aa_file = protein_alignment_folder + "/" + cluster + ".faa"
protein_tree_output = protein_tree_folder + "/" + cluster + ".tre"
nucleotide_tree_output = dna_tree_folder + "/" + cluster + ".tre"
unaligned_DNA.writeToFile(dna_unaligned_folder + "/" + cluster + ".fna", format="fasta")
unaligned_AA.writeToFile(protein_unaligned_folder + "/" + cluster + ".faa", format="fasta")
aligned_DNA.writeToFile(aligned_dna_file, format="fasta")
aligned_AA.writeToFile(aligned_aa_file, format="fasta")
#!/usr/bin/env python # taken from http://pycogent.sourceforge.net/ from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs from cogent.core.moltype import DNA from cogent import LoadSeqs from cogent.app.raxml import build_tree_from_alignment as raxml_build_tree unaligned_seqs = LoadSeqs(filename='data/test2.fasta', aligned=False) aln = mafft_align_unaligned_seqs(unaligned_seqs, DNA) #raxml_tree = raxml_build_tree(aln, DNA) #print raxml_tree
if len(curated_protein_list
) < 2: # Only take those clusters with 3 sequences or more
clusters_too_short.append(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)
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')
