[Bioperl-l] Query re naming / distribution of bio-related module [bio-newbie - be gentle!]

[Heikki Lehvaslaiho]

Simon,

Sorry for chiming in late, but I have been travelling.

Note that we have a convention of naming methods in all lower case
characters, e.g.:


getErrorStr() - returns information on last error

get_error_str()
 
> loadRLFile()

load_rl_file()


It's no big deal, but it helps in the long run if everyone follows the
conventions. See Bio::SimpleAlign module to find out how you can put in
both if you prefer to use the mixed case convention yourself.

Yours,
	-Heikki


On Mon, 2002-04-15 at 13:01, Simon Whitaker wrote:
> On Mon, 15 Apr 2002 08:36:52 +0800 (SGT) Elia Stupka wrote:
> 
> > don't worry we are not known to bite ;)
> 
> Phew. :-)
> 
> > Your module sounds interesting and it would probably be very helpful if
> > you could post some more specs about the input data, all the various
> > methods it has, and the output types, for us to understand better where it
> > fits in the package, and whether it overlaps with some of the other
> > modules you have.
> 
> The data we're working on is arranged in two types of file. A repeat
> length data file contains data on the number of repeats found at a
> number of loci for a number of strains of the organism being examined.
> Data is in comma- or tab-separated format. For example:
> 
>     lgtC,lex2A,lic1,lic2,lic3,strain
>     15,20,33,30,29,1231
>     15,20,34,30,29,1232
>     43,26,39,22,36,1209
>     41,25,39,22,36,1207
> 
> A mutation rate data file maps repeat lengths to their estimated
> mutation rates. For example:
> 
>     10,0.00001
>     11,0.0001
>     12,0.001
>     13,0.01
>     14,0.1
> 
> Here's a breakdown of the public methods (as currently envisaged):
> 
> Constructor:
> 
> new() - no arguments. Creates and initialises a new Bio::MutPhenotyper
> object. (of course :-)
> 
> Member functions:
> 
> getErrorStr() - returns information on last error
> 
> loadRLFile() - takes a filename as an argument. Loads repeat length data
> for this object from that file. Returns number of rows read on success,
> sets an error message (getable with getErrorStr) and returns 0 on
> failure. (If the object already has repeat length data loaded it is
> overwritten.)
> 
> e.g.:
> 
>     my $typer = new Bio::MutPhenotyper;
>     my $rows = $typer->loadRLData("somedata.rl") or die $myTyper->getErrorStr;
> 
> readRLData() - as above, but takes a single line of data as an argument.
> Returns number of fields read on success, sets an error message (getable
> with getErrorStr) and returns 0 on failure.
> 
> loadMRFile() - takes filename as argument. Loads mutation rate data for
> this object from that file. Returns number of rows read on success, sets
> error message and returns 0 on failure. (Basically as above.)
> 
> getRLData() - returns reference to 2D array containing repeat length
> data for the current object
> 
> getMRData() - returns reference to a hash containing mutation rate data.
> 
> calcMutPhenotypes() - no arguments. Calculates mutation phenotypes for
> all strains in the repeat-length data. Returns reference to
> 2-dimensional array of results on success, sets error message and
> returns 0 on failure.
> 
> calcMeanRepeats() - no arguments. Calculates mean and s.d. on repeat
> lengths in the repeat-length data. Returns reference to 2-dimensional
> array of results on success, sets error message and returns 0 on failure.
> 
> calcTotalAlleles() - no arguments. Calculates total number of alleles
> for each locus. Returns reference to 2-dimensional array of results on
> success, sets error message and returns 0 on failure.
> 
> translateToUniqueAlleles() - no arguments. Translates repeat length data
> into unique alleles. Returns reference to 2-dimensional array of results
> on success, sets error message and returns 0 on failure.
> 
> translateToMutRates() - no arguments. Translates repeat length data into
> mutation rates. Returns reference to 2-dimensional array of results on
> success, sets error message and returns 0 on failure.
> 
> 
> All the best,
> 
> Simon
> 
> -- 
> Simon Whitaker
> http://netcetera.org/
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________