[Bioperl-l] Problems parsing Glimmer output

[Chris Fields]

Update to bioperl-live (from CVS).  The Glimmer parser was recently  
revised by Mark Johnson for Glimmer3 output.  I added a few fixes  
myself to correct start/end issues.

chris

On Oct 24, 2007, at 7:25 AM, Martin Burkert wrote:

> Hello,
>
> i can't figure out why my Glimmer files can not be parsed from
> Bio::Tools::Glimmer.
>
> ---- pbglimmer.pl ----
> use strict;
> use Bio::Tools::Glimmer;
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
> my $predictionCount = 0;
>
> while(my $gene = $parser->next_prediction()) {
> 	$predictionCount++;
> 	print $predictionCount.	':' .$gene->display_name().
> 				', '.$gene->start().
> 				', '.$gene->stop()."\n";
> }
> print "Total predictions: ".$predictionCount;
>
> ---- pb4.predict ----
>> pb4
> orf00001     1022     1138  +2     0.90
> orf00002     1655     1131  -3     2.77
> orf00003     1638     2390  +3     3.59
> orf00004     3176     3472  +2     0.30
> orf00006     4395     5561  +3     2.96
> orf00008     5576     8719  +2     2.98
> orf00012     8725    10152  +1     2.96
> orf00013    10906    11019  +1     0.21
> orf00014    12188    12292  +2     2.41
> orf00017    12518    14077  +2     2.97
> orf00019    15356    15246  -3     2.21
> orf00020    17864    17748  -3     0.23
> orf00021    18153    18037  -1     0.32
> orf00023    19253    19462  +2     0.48
> orf00025    21018    20902  -1     0.23
> orf00027    21658    24708  +1     2.92
> orf00030    26115    24898  -1     2.96
> orf00031    26414    26112  -3     3.21
> orf00032    28015    28473  +1     3.54
> orf00033    28044    27223  -1     2.85
> orf00037    30137    30033  -3     2.80
> orf00041    30183    33152  +3     2.98
> orf00045    34860    33637  -1     2.96
> orf00047    35142    34909  -1     2.54
> orf00050    36606    36737  +3     1.44
> orf00052    37616    37789  +2     2.23
> orf00054    37786    40344  +1     2.98
> orf00056    40624    40505  -2     0.79
> orf00057    42508    43890  +1     2.96
> orf00059    44183    44680  +2     1.49
> orf00060    44705    44908  +2     0.05
> orf00063    44920    46632  +1     2.97
> orf00068    47296    47865  +1     0.39
> orf00071    47953    49134  +1     2.90
> orf00072    49208    49318  +2     1.15
> orf00074    51139    51270  +1     1.16
> orf00083    58362    53767  -1     2.99
> orf00088    60846    58783  -1     2.98
> orf00090    63298    61394  -2     2.97
> orf00093    65553    63295  -1     2.98
> orf00095    65959    65588  -2     1.13
> orf00096    66185    65964  -3     2.98
> orf00098    66610    66933  +1     0.11
> orf00099    67371    67658  +3     0.27
> orf00102    71019    68134  -1     2.98
> orf00103    71825    72628  +2     2.71
> orf00105    75062    73740  -3     2.96
> orf00106    75817    76221  +1     0.73
> orf00109    78206    76734  -3     2.92
> orf00113      198    79299  -3     4.22
>
>
> The program always outputs "Total predictions: 0".
>
> I also tried to force the parsing format to be just 'Glimmer'
> (prokaryotic) and not 'GlimmerHmm'  with:
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', - 
> format =>
> 'Glimmer');
>
> The pb4.predict was generated by glimmer3.02. I also tried to parse an
> output from glimmer2.X, but without success.
>
> Printing $parser with Data::Dumper outputs:
>
> $VAR1 = bless( {
>                  '_file' => 'pb4.predict',
>                  '_preds_parsed' => 0,
>                  '_analysis_date' => undef,
>                  '_root_cleanup_methods' => [
>                                               sub { "DUMMY" }
>                                             ],
>                  '_analysis_sbjct' => undef,
>                  '_analysis_progVersion' => undef,
>                  '_flush_on_write' => 1,
>                  '_analysis_prog' => undef,
>                  '_filehandle' => \*Symbol::GEN0,
>                  '_analysis_query' => undef,
>                  '_root_verbose' => 0,
>                  '_preds' => []
>                }, 'Bio::Tools::Glimmer' );
>
> My installation:
>
> Perl v5.8.8 built for MSWin32-x86-multi-thread
> Bioperl 1.4
>
> Thank you.
>
> -- 
> Viele Grüße,
>
> MARTIN BURKERT
> mailto:martin.burkert at uni-bielefeld.de
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign