Glimmer: ensure have Bio.Seq for reverse complement

#123

Author: chapmanb

biopython/glimmer_to_proteins.py

@@ -21,7 +21,7 @@
 import operator
 from functools import reduce
 
-from Bio import SeqIO
+from Bio import SeqIO, Seq
 from Bio.SeqRecord import SeqRecord
 
 def main(glimmer_file, ref_file):
@@ -41,7 +41,7 @@ def protein_recs(glimmer_file, ref_rec):
             seq_exons = []
             for start, end in exons:
                 seq_exons.append(ref_rec.seq[start:end])
-            gene_seq = reduce(operator.add, seq_exons, "")
+            gene_seq = Seq.Seq(str(reduce(operator.add, seq_exons, "")))
             if strand == '-':
                 gene_seq = gene_seq.reverse_complement()
             protein_seq = gene_seq.translate()

biopython/glimmergff_to_proteins.py

@@ -19,7 +19,7 @@
 import operator
 from functools import reduce
 
-from Bio import SeqIO
+from Bio import SeqIO, Seq
 from Bio.SeqRecord import SeqRecord
 
 from BCBio import GFF
@@ -44,7 +44,7 @@ def protein_recs(glimmer_file, ref_recs):
                     seq_exons.append(rec.seq[
                         cds.location.nofuzzy_start:
                         cds.location.nofuzzy_end])
-                gene_seq = reduce(operator.add, seq_exons, "")
+                gene_seq = Seq.Seq(str(reduce(operator.add, seq_exons, "")))
                 if feature.strand == -1:
                     gene_seq = gene_seq.reverse_complement()
                 protein_seq = gene_seq.translate()