CloneSet350

Bio/GenBank/__init__.py

BioSQL/BioSeq.py

        # Historically a join on the reverse strand has been represented
        # in Biopython with both the parent SeqFeature and its children
        # (the exons for a CDS) all given a strand of -1.  Likewise, for
        # a join feature on the forward strand they all have strand +1.
        # However, we must also consider evil mixed strand examples like
        # this, join(complement(69611..69724),139856..140087,140625..140650)
        strands = set(sf.strand for sf in cur_feature.sub_features) 
        if len(strands)==1: 
            cur_feature.strand = cur_feature.sub_features[0].strand 
        else: 
            cur_feature.strand = None # i.e. mixed strands

            # To get the parent strand (as done when parsing GenBank files),
            # need to consider evil mixed strand examples like this,
            # join(complement(69611..69724),139856..140087,140625..140650)
            strands = set(sf.strand for sf in feature.sub_features) 
            if len(strands)==1: 
                feature.strand = feature.sub_features[0].strand 
            else: 
                feature.strand = None # i.e. mixed strands

# Historically a join on the reverse strand has been represented
# in Biopython with both the parent SeqFeature and its children
# (the exons for a CDS) all given a strand of -1.  Likewise, for
# a join feature on the forward strand they all have strand +1.
# However, we must also consider evil mixed strand examples like
# this, join(complement(69611..69724),139856..140087,140625..140650)
# To get the parent strand (as done when parsing GenBank files),
# need to consider evil mixed strand examples like this,
# join(complement(69611..69724),139856..140087,140625..140650)
strands = set(sf.strand for sf in [[#variable2e7c6fe0]].sub_features) 
if len(strands)==1:
   [[#variable2e7c6fe0]].strand = [[#variable2e7c6fe0]].sub_features[0].strand 
else:
   [[#variable2e7c6fe0]].strand = None # i.e. mixed strands
 

cur_feature 

feature