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Improve statistics output #1619

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merged 4 commits into from
Apr 8, 2024
Merged

Improve statistics output #1619

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dabf8bf
Fix bug when running Stats without version data
nuno-agostinho Feb 21, 2024
55a1812
Fix input when using input_data
nuno-agostinho Feb 21, 2024
966467a
Merge remote-tracking branch 'upstream/postreleasefix/112' into bug/f…
nuno-agostinho Mar 4, 2024
cab17c4
Merge remote-tracking branch 'upstream/postreleasefix/112' into bug/f…
nuno-agostinho Apr 8, 2024
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36 changes: 27 additions & 9 deletions modules/Bio/EnsEMBL/VEP/Stats.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -643,13 +643,23 @@ sub generate_run_stats {
}
}

# Distinguish input source
my ($input, $input_label);
if ($self->param('input_file') eq *Bio::EnsEMBL::VEP::Runner::IN) {
$input = $self->param('input_data');
$input_label = 'Input data';
} else {
$input = $self->param('input_file');
$input_label = 'Input file';
}

my @return = (
['Species', $self->species],
['Command line options', '<pre>'.join(" ", @opts).'</pre>'],
['Start time', $self->start_time],
['End time', $self->end_time],
['Run time', $self->run_time." seconds"],
['Input file', "<pre>".$self->param('input_file')."</pre>"],
[$input_label, "<pre>".$input."</pre>"],
['Output file', "<pre>".$self->param('output_file')."</pre>"],
);

Expand Down Expand Up @@ -684,7 +694,7 @@ sub generate_run_stats {

sub generate_data_version {
my $self = shift;
my %version_data = %{ $self->{info}->{version_data} };
my %version_data = %{ $self->{info}->{version_data} } if $self->{info}->{version_data};
my @return = map { [ $_, $version_data{$_} ] } sort keys %version_data;
return \@return;
}
Expand Down Expand Up @@ -802,8 +812,12 @@ sub dump_text {
print $fh "[VEP run statistics]\n";
print $fh join("\t", map {s/\<.+?\>//g; $_} @{$_})."\n" for @{$finished_stats->{run_stats}};

print $fh "[Data version]\n";
print $fh join("\t", map {s/\<.+?\>//g; $_} @{$_})."\n" for @{$finished_stats->{data_version}};
print $fh "\n[Data version]\n";
if (@{$finished_stats->{data_version}}) {
print $fh join("\t", map {s/\<.+?\>//g; $_} @{$_})."\n" for @{$finished_stats->{data_version}};
} else {
print $fh "No data version information available.\n";
}

print $fh "\n[General statistics]\n";
print $fh join("\t", map {s/\<.+?\>//g; $_} grep {defined($_)} @{$_})."\n" for @{$finished_stats->{general_stats}};
Expand Down Expand Up @@ -864,11 +878,15 @@ sub dump_html {
join('', map {'<tr>'.join('', map {'<td>'.$_.'</td>'} @$_).'</tr>'} @{$finished_stats->{run_stats}}).
'</table>';

print $fh
'<h3 id="data_version">Data version</h3>'.
'<table class="stats_table">'.
join('', map {'<tr>'.join('', map {'<td>'.$_.'</td>'} @$_).'</tr>'} @{$finished_stats->{data_version}}).
'</table>';
print $fh '<h3 id="data_version">Data version</h3>';
if (@{$finished_stats->{data_version}}) {
print $fh
'<table class="stats_table">'.
join('', map {'<tr>'.join('', map {'<td>'.$_.'</td>'} @$_).'</tr>'} @{$finished_stats->{data_version}}).
'</table>';
} else {
print $fh 'No data version information available.';
}

# vars in/out stats
print $fh
Expand Down