From dddeaffc6146a23aa52b98384ef01515ebe77a23 Mon Sep 17 00:00:00 2001
From: Steve Trevanion <st3@sanger.ac.uk>
Date: Wed, 11 Feb 2009 16:25:03 +0000
Subject: [PATCH] date format method added
---
.../Bio/EnsEMBL/Utils/ConversionSupport.pm | 110 ++++++++++++------
1 file changed, 75 insertions(+), 35 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index 12402bce84..b195e2d223 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -238,8 +238,10 @@ sub get_common_params {
=head2 get_loutre_params
- Example : my @allowed_params = $self->get_loutre_params, 'extra_param';
- Description : Returns a list of commonly used parameters in for working with a loutre db
+ Arg : (optional) return a list to parse or not
+ Example : $support->parse_extra_options($support->get_loutre_params('parse'))
+ Description : Returns a list of commonly used loutre db parameters - parse option is
+ simply used to distinguish between reporting and parsing parameters
Return type : Array - list of common parameters
Exceptions : none
Caller : general
@@ -247,13 +249,25 @@ sub get_common_params {
=cut
sub get_loutre_params {
- return qw(
- loutrehost
- loutreport
- loutreuser
- loutrepass
- loutredbname
- );
+ my ($self,$p) = @_;
+ if ($p) {
+ return qw(
+ loutrehost=s
+ loutreport=s
+ loutreuser=s
+ loutrepass=s
+ loutredbname=s
+ );
+ }
+ else {
+ return qw(
+ loutrehost
+ loutreport
+ loutreuser
+ loutrepass
+ loutredbname
+ );
+ }
}
=head2 remove_vega_params
@@ -293,9 +307,9 @@ sub confirm_params {
print "Running script with these parameters:\n\n";
print $self->list_all_params;
- if ($self->param('host') eq 'web-4-11') {
+ if ($self->param('host') eq 'ensdb-1-10') {
# ask user if he wants to proceed
- exit unless $self->user_proceed("**************\n\n You're working on web-4-11! Is that correct and you want to continue ?\n\n**************");
+ exit unless $self->user_proceed("**************\n\n You're working on ensdb-1-10! Is that correct and you want to continue ?\n\n**************");
}
else {
# ask user if he wants to proceed
@@ -362,7 +376,6 @@ sub create_commandline_options {
if ($settings->{'allowed_params'}) {
# exclude params explicitly stated
my %exclude = map { $_ => 1 } @{ $settings->{'exclude'} || [] };
-
foreach my $param ($self->allowed_params) {
unless ($exclude{$param}) {
my ($first, @rest) = $self->param($param);
@@ -387,7 +400,6 @@ sub create_commandline_options {
foreach my $param (keys %param_hash) {
$options_string .= sprintf("--%s %s ", $param, $param_hash{$param});
}
-
return $options_string;
}
@@ -689,8 +701,17 @@ sub get_database {
-dbname => $self->param("${prefix}dbname"),
-group => $database,
);
-
- # explicitely set the dnadb to itself - by default the Registry assumes
+ #can use this approach to get dna from another db
+# my $dna_db = $adaptors{$database}->new(
+# -host => 'otterlive',
+# -port => '3301',
+# -user => $self->param("${prefix}user"),
+# -pass => $self->param("${prefix}pass"),
+# -dbname => 'loutre_human',
+# );
+# $dba->dnadb($dna_db);
+
+ # otherwise explicitely set the dnadb to itself - by default the Registry assumes
# a group 'core' for this now
$dba->dnadb($dba);
@@ -928,26 +949,25 @@ sub get_chrlength {
=cut
sub get_ensembl_chr_mapping {
- my ($self, $dba, $version) = @_;
- $dba ||= $self->dba;
- throw("get_ensembl_chr_mapping should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n") unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));
-
- my $sa = $dba->get_SliceAdaptor;
- my @chromosomes = map { $_->seq_region_name }
- @{ $sa->fetch_all('chromosome', $version) };
-
- my %chrs;
- foreach my $chr (@chromosomes) {
- my $sr = $sa->fetch_by_region('chromosome', $chr, undef, undef, undef, $version);
- my ($ensembl_name_attr) = @{ $sr->get_all_Attributes('ensembl_name') };
- if ($ensembl_name_attr) {
- $chrs{$chr} = $ensembl_name_attr->value;
- } else {
- $chrs{$chr} = $chr;
- }
+ my ($self, $dba, $version) = @_;
+ $dba ||= $self->dba;
+ throw("get_ensembl_chr_mapping should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n") unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));
+
+ my $sa = $dba->get_SliceAdaptor;
+ my @chromosomes = map { $_->seq_region_name }
+ @{ $sa->fetch_all('chromosome', $version) };
+
+ my %chrs;
+ foreach my $chr (@chromosomes) {
+ my $sr = $sa->fetch_by_region('chromosome', $chr, undef, undef, undef, $version);
+ my ($ensembl_name_attr) = @{ $sr->get_all_Attributes('ensembl_name') };
+ if ($ensembl_name_attr) {
+ $chrs{$chr} = $ensembl_name_attr->value;
+ } else {
+ $chrs{$chr} = $chr;
}
-
- return \%chrs;
+ }
+ return \%chrs;
}
=head2 get_taxonomy_id
@@ -1186,7 +1206,7 @@ sub log {
Arg[1] : String $txt - the warning text to log
Arg[2] : Int $indent - indentation level for log message
- Arg[2] : Bool - add a line break before warning if true
+ Arg[3] : Bool - add a line break before warning if true
Example : my $log = $support->log_filehandle;
$support->log_warning('Log foo.\n', 1);
Description : Logs a message via $self->log and increases the warning counter.
@@ -1438,6 +1458,26 @@ sub date {
return strftime "%Y-%m-%d %T", localtime;
}
+=head2 format_time
+
+ Example : print $support->format_time($gene->modifed_date) . "\n";
+ Description : Prints timestamps from the database
+ Return type : String - nicely formatted time stamp
+ Exceptions : none
+ Caller : general
+
+=cut
+
+
+sub date_format {
+ my( $self, $time, $format ) = @_;
+ my( $d,$m,$y) = (localtime($time))[3,4,5];
+ my %S = ('d'=>sprintf('%02d',$d),'m'=>sprintf('%02d',$m+1),'y'=>$y+1900);
+ (my $res = $format ) =~s/%(\w)/$S{$1}/ge;
+ return $res;
+}
+
+
=head2 mem
Example : print "Memory usage: " . $support->mem . "\n";
--
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