[Bioperl-l] Problems parsing Glimmer output

Martin Burkert martin.burkert at uni-bielefeld.de
Wed Oct 24 08:25:13 EDT 2007


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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