[EMBOSS] fuzznuc option report

Peter Rice pmr at ebi.ac.uk
Tue Nov 4 15:30:34 UTC 2008

Veronique.Martin at jouy.inra.fr wrote:
  > With fuzznuc how can I get in the report, the total sequences that there
> are in my sequence list.
> At the end of the report, there is just the total of sequences found by 
> fuzznuc and the total hitcount, but I would like to known, how many 
> sequence was in my list at the begining.
> In the following example my sequence list was 50 sequences.
> #---------------------------------------
> # Total_sequences: 40
> # Total_hitcount: 44
> #---------------------------------------
> Is it possible to have something like that? 
> -------------------------------------------
>  Total finds:              40
>  Total hitcount:           44
>  Total sequences:          50
> --------------------------------------------

Interesting question. It is more difficult than it seems.

In the current output, "Total_sequences" is the number of times the report 
output has been called. Fuzznuc (and other programs) only call report 
output functions when they have something to report. Only the calling 
program (fuzznuc) knows how many sequences were read.

However, the tail is written when the report file is closed, so we can 
simply pass the total number of input sequences to a version of 
ajReportClose, or add a function that sets a value for the report tail.

We will add it to the next release.


Peter Rice

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