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  1. OMG Issue

BSA — clarification of strand_type and CompositeSeqRegions

  • Key: BSA-51
  • Legacy Issue Number: 3962
  • Status: closed  
  • Source: ( Philip Lijnzaad)
  • Summary:

    The methods

    BioSequence.seq_interval(in Interval the_interval),
    NucleotideSequence.translate_seq_region(in SeqRegion seq_region, ...)
    NucleotideSequence.reverse_complement_interval(in Interval the_interval)

    may all be called using a SeqRegion. In this case, the StrandType may be
    minus, and if that is the case, the string returned (for seq_interval) or the
    string 'transformed' (the other cases) should be taken as
    reverse-complemented. In the last case, this will result in a no-op,
    i.e. the strand_type leads to reverse-complementing, which is then
    reverse-complementing due to the semantics of the method, ending up in the
    same string that wouuld be had from seq_interval().

    We suggest adding verbiage to explain these semantics (if, of course, everyone
    agrees that this is the expected behaviour!)

    Similar to this issue is that all CompositeSeqRegions are expected to be
    translated in a depth-first traversal, along each node of the tree
    represented by the CompositeSeqRegions. This includes those nodes that have
    region_operator == JOIN or ORDER.

  • Reported: BSA 1.0b1 — Tue, 17 Oct 2000 04:00 GMT
  • Disposition: Resolved — BSA 1.0
  • Disposition Summary:


  • Updated: Fri, 6 Mar 2015 20:57 GMT