[Bioperl-l] Bio::MapIO::mapmaker

[Brian Osborne]

Daniel,

I've never used this module but this certainly doesn't sound right. Can you
submit this as a bug so your observation isn't "lost"? Please attach your
input file as well, I will look into it.

Brian O.


On 11/2/05 8:52 AM, "Daniel Lang" <daniel.lang at biologie.uni-freiburg.de>
wrote:

> Hi,
> I found something odd when working with Bio::MapIO::mapmaker (1.5.1 but
> also todays cvs version) ...
> Is it on purpose, that the parser "forgets" the last marker of a map?
> For example when parsing a map like:
> Map:
>   mapname=THE_NAME_OF_MAP
>   Markers          Distance
>   1  bnl5.62a         35.3 cM coremarker
>   2  npi406           15.6 cM EST
>   3  npi439a          27.2 cM
>   4  dpg11            30.7 cM ssr
>   5  bnl7.21a           33 cM
>   6  bnl23b            8.6 cM coremarker
>   7  umc58           107.9 cM
>   8  npi605a          26.5 cM EST
>   9  npi120             19 cM ssr
>   10  npi615           19.5 cM coremarker
>   11  npi407             14 cM
>   12  npi241a          45.2 cM
>   13  bnl6.32       ---------- RflP
> 
> marker n°13 is always left out when iterating over the map i.e. like this:
> #!/usr/bin/perl
> #test script to read mapmaker outputs
> use strict;
> use warnings;
> use Bio::MapIO;
> 
> my $mapio = new Bio::MapIO(-format => "mapmaker",
>                            -file   => $ARGV[0]);
> while (my $map = $mapio->next_map) {
>         last unless $map->length;
>         print $map->type ." ". $map->length ." " . $map->unique_id ."\n";
>         foreach my $marker ( $map->each_element ) {
>                 print $marker->name ."\t" .$marker->position->order
> ."\t", $marker->position->value , "\t", $marker->position->numeric ,"\n";
>         }
> }
> Output:
> ./readMap.pl test.map
> Genetic 382.5 1
> bnl5.62a        1       35.3    35.3
> npi406  2       50.9    50.9
> npi439a 3       78.1    78.1
> dpg11   4       108.8   108.8
> bnl7.21a        5       141.8   141.8
> bnl23b  6       150.4   150.4
> umc58   7       258.3   258.3
> npi605a 8       284.8   284.8
> npi120  9       303.8   303.8
> npi615  10      323.3   323.3
> npi407  11      337.3   337.3
> npi241a 12      382.5   382.5
> 
> Additionally, the iterator method Bio::MapIO::mapmaker::next_map doesn´t
> terminate correctly (Hence my test for the length of the map in the
> while loop).
> 
> Thanks in advance!
> Daniel:)
>