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Bio.Alphabet no longer available in Biopython #28

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Bio.Alphabet no longer available in Biopython #28

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8 changes: 5 additions & 3 deletions scripts/snppar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
from Bio import SeqIO, AlignIO
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC, generic_dna
#from Bio.Alphabet import IUPAC, generic_dna
from Bio.SeqRecord import SeqRecord
from Bio.Seq import _dna_complement_table as dna_complement_table
from Bio.Data.CodonTable import TranslationError
Expand Down Expand Up @@ -1878,7 +1878,8 @@ def getCodons(positionInCodon,genestrand,snpPosition,derived,ancestral,derived_g
elif genestrand == -1:
codonseq[positionInCodon-1] = ancestral.translate(dna_complement_table)
codonseq = getAncestralBasesReverse(codonseq,positionInCodon,codon,snp_list,node_snptable,ancestral_group)
ancestral_codon = Seq(''.join(codonseq),IUPAC.unambiguous_dna)
#ancestral_codon = Seq(''.join(codonseq),IUPAC.unambiguous_dna)
ancestral_codon = Seq(''.join(codonseq))
# mutate with current SNP
# again checking other bases in codon
if genestrand == 1:
Expand All @@ -1887,7 +1888,8 @@ def getCodons(positionInCodon,genestrand,snpPosition,derived,ancestral,derived_g
elif genestrand == -1:
codonseq[positionInCodon-1] = derived.translate(dna_complement_table)
codonseq = getDerivedBasesReverse(codonseq,positionInCodon,codon,snp_list,node_snptable,derived_group,strains,snptable)
derived_codon = Seq(''.join(codonseq),IUPAC.unambiguous_dna)
#derived_codon = Seq(''.join(codonseq),IUPAC.unambiguous_dna)
derived_codon = Seq(''.join(codonseq))

# Translate codons; codons containing ambigous bases cannot always be translated,
# in these cases set amino acid (AA) to None
Expand Down