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#231 cons produces "-" for two letters with same frequecy

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nobody
Applications (75)
5
2012-09-11
2012-09-11
Nagaev Boris
No

Command:
cons -plurality 0.0 -setcase 9.9 cons-bug.fasta

Output:
ATGAGggGGGGggggg-aGTGAGCGACGTCGCGTGAAGCGCGGCTATCTTCGCTTCGCCA

Both "G" and "A" get score 3 at column 17, but cons produced "-" for this column.
"-" is not described as possible output in the cons documentation. We propose to print one of input letters ("G" or "A") instead.

EMBOSS 6.3.1 (Debian)

Discussion

  • Nagaev Boris

    Nagaev Boris - 2012-09-11

    input file for cons

     
    cons-bug.fasta

  • Peter Rice

    Peter Rice - 2012-09-19

    hanks for spoting this one.

    This situation is addressed by prettyplot using the collisions option which allows one of the alternatives to be used in the consensus. We used the same functions for cons but some additional parameters will be needed to ensure a consensus is filled in.

    Certainly something has to be chosen because the cons output should be a valid sequence and '-' is treated as a gap character.