diff --git a/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
index 2f92d8d5ca0889628bb48c43b11119981d318ee6..cb3bf471c9f99a721bd73f1ab4c7539736bfa11d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
@@ -160,20 +160,32 @@ sub fetch_all_by_Slice {
my $best_ratio = undef;
my $density_type = undef;
+ my $best_ratio_large = undef;
+ my $density_type_large = undef;
foreach my $dt (@dtypes) {
- my $ratio;
- if($dt->block_size() < $wanted_block_size) {
- $ratio = $wanted_block_size/$dt->block_size();
+ my $ratio = $wanted_block_size/$dt->block_size();
+
+ # we prefer to use a block size that's smaller than the required one
+ # (better results on interpolation). remember larger block sizes though
+ # in case there is no smaller one in the database
+ if ($ratio < 1) {
+ if(!defined($best_ratio_large) || $ratio > $best_ratio_large) {
+ $best_ratio_large = $ratio;
+ $density_type_large = $dt;
+ }
} else {
- $ratio = $dt->block_size()/$wanted_block_size;
- }
-
- if(!defined($best_ratio) || $ratio < $best_ratio) {
- $best_ratio = $ratio;
- $density_type = $dt;
+ if(!defined($best_ratio) || $ratio < $best_ratio) {
+ $best_ratio = $ratio;
+ $density_type = $dt;
+ }
}
}
+ # fall back to larger block size
+ unless ($best_ratio) {
+ $best_ratio = $best_ratio_large;
+ $density_type = $density_type_large;
+ }
#the ratio was not good enough, or this logic name was not in the
#density type table, return an empty list
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 0d15e5bc19555fe8dc83274d25dcc6bf39c56f9d..a2b47c0947983a4c60919f289cc6cfeac736f57c 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -524,6 +524,9 @@ sub type {
'Ig_pseudogene_segment.NOVEL' => 'Ig_Pseudogene_Segment',
'Ig_segment.KNOWN' => 'Ig_Segment',
'Ig_segment.NOVEL' => 'Ig_Segment',
+ 'Known_in_progress.KNOWN' => 'Known_in_progress',
+ 'Novel_CDS_in_progress.KNOWN' => 'Novel_CDS_in_progress',
+ 'Novel_CDS_in_progress.NOVEL' => 'Novel_CDS_in_progress',
);
my $bio_conf = $self->biotype.".".$self->confidence;
if ($typemap{$bio_conf}) {
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index 15dbaa902b0ad6820fc940f222d10bad4dfe9d49..5251d7cab6d6cb5f838bc01126937cc898f02535 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -51,6 +51,7 @@ use Text::Wrap;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use FindBin qw($Bin $Script);
use POSIX qw(strftime);
+use Cwd qw(abs_path);
=head2 new
@@ -66,7 +67,7 @@ use POSIX qw(strftime);
sub new {
my $class = shift;
- (my $serverroot = shift) or throw("You must supply a serverroot");
+ (my $serverroot = shift) or throw("You must supply a serverroot.");
my $self = {
'_serverroot' => $serverroot,
'_param' => { interactive => 1 },
@@ -103,10 +104,10 @@ sub parse_common_options {
'port|dbport|db_port=n',
'user|dbuser|db_user=s',
'pass|dbpass|db_pass=s',
- 'driver|dbdriver|db_driver=s',
'conffile|conf=s',
'logfile|log=s',
'logpath=s',
+ 'logappend|log_append=s',
'verbose|v=s',
'interactive|i=s',
'dry_run|dry|n=s',
@@ -115,6 +116,7 @@ sub parse_common_options {
# reads config file
my $conffile = $h{'conffile'} || $self->serverroot . "/conf/Conversion.ini";
+ $conffile = abs_path($conffile);
if (-e $conffile) {
open(CONF, $conffile) or throw(
"Unable to open configuration file $conffile for reading: $!");
@@ -129,6 +131,7 @@ sub parse_common_options {
next unless (/(\w\S*)\s*=\s*(.*)/);
$self->param($1, $2);
}
+ $self->param('conffile', $conffile);
} else {
warning("Unable to open configuration file $conffile for reading: $!");
}
@@ -162,6 +165,65 @@ sub parse_extra_options {
return(1);
}
+=head2 allowed_params
+
+ Arg[1-N] : (optional) List of allowed parameters to set
+ Example : my @allowed = $self->allowed_params(qw(param1 param2));
+ Description : Getter/setter for allowed parameters. This is used by
+ $self->confirm_params() to avoid cluttering of output with
+ conffile entries not relevant for a given script. You can use
+ $self->get_common_params() as a shortcut to set them.
+ Return type : Array - list of allowed parameters
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub allowed_params {
+ my $self = shift;
+
+ # setter
+ if (@_) {
+ @{ $self->{'_allowed_params'} } = @_;
+ }
+
+ # getter
+ if (ref($self->{'_allowed_params'}) eq 'ARRAY') {
+ return @{ $self->{'_allowed_params'} };
+ } else {
+ return ();
+ }
+}
+
+=head2 get_common_params
+
+ Example : my @allowed_params = $self->get_common_params, 'extra_param';
+ Description : Returns a list of commonly used parameters in the conversion
+ scripts. Shortcut for setting allowed parameters with
+ $self->allowed_params().
+ Return type : Array - list of common parameters
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub get_common_params {
+ return qw(
+ conffile
+ dbname
+ host
+ port
+ user
+ pass
+ logpath
+ logfile
+ logappend
+ verbose
+ interactive
+ dry_run
+ );
+}
+
=head2 confirm_params
Example : $support->confirm_params;
@@ -202,22 +264,107 @@ sub list_all_params {
my $txt = sprintf " %-20s%-40s\n", qw(PARAMETER VALUE);
$txt .= " " . "-"x70 . "\n";
$Text::Wrap::colums = 72;
- foreach my $key (sort keys %{ $self->{'_param'} }) {
+ my @params = $self->allowed_params;
+ foreach my $key (@params) {
my @vals = $self->param($key);
- $txt .= Text::Wrap::wrap( sprintf(' %-20s', $key),
- ' 'x24,
- join(", ", @vals)
- ) . "\n";
+ if (@vals) {
+ $txt .= Text::Wrap::wrap( sprintf(' %-20s', $key),
+ ' 'x24,
+ join(", ", @vals)
+ ) . "\n";
+ }
}
$txt .= "\n";
return $txt;
}
+=head2 create_commandline_options
+
+ Arg[1] : Hashref $settings - hashref describing what to do
+ Allowed keys:
+ allowed_params => 0|1 # use all allowed parameters
+ exclude => [] # listref of parameters to exclude
+ replace => {param => newval} # replace value of param with
+ # newval
+ Example : $support->create_commandline_options({
+ allowed_params => 1,
+ exclude => ['verbose'],
+ replace => { 'dbname' => 'homo_sapiens_vega_33_35e' }
+ });
+ Description : Creates a commandline options string that can be passed to any
+ other script using ConversionSupport.
+ Return type : String - commandline options string
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub create_commandline_options {
+ my ($self, $settings) = @_;
+ my %param_hash;
+
+ # get all allowed parameters
+ if ($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);
+ next unless (defined($first));
+
+ if (@rest) {
+ $first = join(",", $first, @rest);
+ }
+ $param_hash{$param} = $first;
+ }
+ }
+
+ }
+
+ # replace values
+ foreach my $key (keys %{ $settings->{'replace'} || {} }) {
+ $param_hash{$key} = $settings->{'replace'}->{$key};
+ }
+
+ # create the commandline options string
+ my $options_string;
+ foreach my $param (keys %param_hash) {
+ $options_string .= sprintf("--%s %s ", $param, $param_hash{$param});
+ }
+
+ return $options_string;
+}
+
+=head2 check_required_params
+
+ Arg[1-N] : List @params - parameters to check
+ Example : $self->check_required_params(qw(dbname host port));
+ Description : Checks $self->param to make sure the requested parameters
+ have been set. Dies if parameters are missing.
+ Return type : true on success
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub check_required_params {
+ my ($self, @params) = @_;
+ my @missing = ();
+ foreach my $param (@params) {
+ push @missing, $param unless $self->param($param);
+ }
+ if (@missing) {
+ throw("Missing parameters: @missing.\nYou must specify them on the commandline or in your conffile.\n");
+ }
+ return(1);
+}
+
=head2 user_proceed
Arg[1] : (optional) String $text - notification text to present to user
Example : # run a code snipped conditionally
- if ($support->user_proceed("Run the next code snipped?") {
+ if ($support->user_proceed("Run the next code snipped?")) {
# run some code
}
@@ -311,10 +458,10 @@ sub comma_to_list {
return(1);
}
-=head2 list_to_file
+=head2 list_or_file
Arg[1] : Name of parameter to parse
- Example : $support->list_to_file('gene_stable_id');
+ Example : $support->list_or_file('gene_stable_id');
Description : Determines whether a parameter holds a list or it is a filename
to read the list entries from.
Return type : true on success
@@ -371,6 +518,7 @@ sub param {
$self->{'_param'}->{$name} = shift;
} else {
# list of values
+ undef $self->{'_param'}->{$name};
@{ $self->{'_param'}->{$name} } = @_;
}
}
@@ -444,6 +592,8 @@ sub serverroot {
Arg[1] : String $database - the type of database to connect to
(eg core, otter)
+ Arg[2] : (optional) String $prefix - the prefix used for retrieving the
+ connection settings from the configuration
Example : my $db = $support->get_database('core');
Description : Connects to the database specified.
Return type : DBAdaptor of the appropriate type
@@ -455,11 +605,19 @@ sub serverroot {
sub get_database {
my $self = shift;
my $database = shift or throw("You must provide a database");
- $self->check_required_params(qw(host port user pass dbname));
+ my $prefix = shift;
+ $self->check_required_params(
+ "${prefix}host",
+ "${prefix}port",
+ "${prefix}user",
+ # "${prefix}pass", not required since might be empty
+ "${prefix}dbname",
+ );
my %adaptors = (
core => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
ensembl => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ evega => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
otter => 'Bio::Otter::DBSQL::DBAdaptor',
vega => 'Bio::Otter::DBSQL::DBAdaptor',
);
@@ -468,37 +626,88 @@ sub get_database {
$self->dynamic_use($adaptors{$database});
my $dba = $adaptors{$database}->new(
- -host => $self->param('host'),
- -port => $self->param('port'),
- -user => $self->param('user'),
- -pass => $self->param('pass'),
- -dbname => $self->param('dbname'),
+ -host => $self->param("${prefix}host"),
+ -port => $self->param("${prefix}port"),
+ -user => $self->param("${prefix}user"),
+ -pass => $self->param("${prefix}pass"),
+ -dbname => $self->param("${prefix}dbname"),
+ -group => $database,
);
+ $self->{'_dba'}->{$database} = $dba;
+ $self->{'_dba'}->{'default'} = $dba unless $self->{'_dba'}->{'default'};
+ return $self->{'_dba'}->{$database};
+}
+
+=head2 get_glovar_database
+
+ Example : my $dba = $support->get_glovar_database;
+ Description : Connects to the Glovar database.
+ Return type : Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor
+ Exceptions : thrown if no connection to a core db exists
+ Caller : general
+
+=cut
+
+sub get_glovar_database {
+ my $self = shift;
+ $self->check_required_params(qw(
+ glovarhost
+ glovarport
+ glovaruser
+ glovarpass
+ glovardbname
+ oracle_home
+ ld_library_path
+ glovar_snp_consequence_exp
+ ));
+
+ # check for core dbadaptor
+ my $core_db = $self->dba;
+ unless ($core_db && (ref($core_db) =~ /Bio::.*::DBSQL::DBAdaptor/)) {
+ $self->log_error("You have to connect to a core db before you can get a glovar dbadaptor.\n");
+ exit;
+ }
+
+ # setup Oracle environment
+ $ENV{'ORACLE_HOME'} = $self->param('oracle_home');
+ $ENV{'LD_LIBRARY_PATH'} = $self->param('ld_library_path');
+
+ # connect to Glovar db
+ $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor');
+ my $dba = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
+ -host => $self->param("glovarhost"),
+ -port => $self->param("glovarport"),
+ -user => $self->param("glovaruser"),
+ -pass => $self->param("glovarpass"),
+ -dbname => $self->param("glovardbname"),
+ -group => 'glovar',
+ );
+
+ # setup adaptor inter-relationships
+ $dba->dnadb($core_db);
+ $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::GlovarSNPAdaptor');
+ my $glovar_snp_adaptor = $dba->get_GlovarSNPAdaptor;
+ $glovar_snp_adaptor->consequence_exp($self->param('glovar_snp_consequence_exp'));
+ $core_db->add_ExternalFeatureAdaptor($glovar_snp_adaptor);
+
return $dba;
}
-=head2 check_required_params
+=head2 dba
- Arg[1-N] : List @params - parameters to check
- Example : $self->check_required_params(qw(dbname host port));
- Description : Checks $self->param to make sure the requested parameters
- have been set. Dies if parameters are missing.
- Return type : true on success
+ Arg[1] : (optional) String $database - type of db apaptor to retrieve
+ Example : my $dba = $support->dba;
+ Description : Getter for database adaptor. Returns default (i.e. created
+ first) db adaptor if no argument is provided.
+ Return type : Bio::EnsEMBL::DBSQL::DBAdaptor or Bio::Otter::DBSQL::DBAdaptor
Exceptions : none
Caller : general
=cut
-sub check_required_params {
- my ($self, @params) = @_;
- my @missing = ();
- foreach my $param (@params) {
- push @missing, $param unless $self->param($param);
- }
- if (@missing) {
- throw("Missing parameters: @missing.\nYou must specify them on the commandline or in your conffile.\n");
- }
- return(1);
+sub dba {
+ my ($self, $database) = shift;
+ return $self->{'_dba'}->{$database} || $self->{'_dba'}->{'default'};
}
=head2 dynamic_use
@@ -531,7 +740,8 @@ sub dynamic_use {
=head2 get_chrlength
- Arg[1] : Bio::EnsEMBL::DBSQL::DBAdaptor $dba
+ Arg[1] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $dba
+ Arg[2] : (optional) String $version - coord_system version
Example : my $chr_length = $support->get_chrlength($dba);
Description : Get all chromosomes and their length from the database. Return
chr_name/length for the chromosomes the user requested (or all
@@ -543,15 +753,15 @@ sub dynamic_use {
=cut
sub get_chrlength {
- my ($self, $dba) = @_;
+ my ($self, $dba, $version) = @_;
+ $dba ||= $self->dba;
throw("get_chrlength should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n")
unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));
my $sa = $dba->get_SliceAdaptor;
my @chromosomes = map { $_->seq_region_name }
- @{ $sa->fetch_all('chromosome') };
- my %chr = map { $_ => $sa->fetch_by_region('chromosome', $_)->length }
- @chromosomes;
+ @{ $sa->fetch_all('chromosome', $version) };
+ my %chr = map { $_ => $sa->fetch_by_region('chromosome', $_, undef, undef, undef, $version)->length } @chromosomes;
my @wanted = $self->param('chromosomes');
if (@wanted) {
@@ -598,6 +808,7 @@ sub get_chrlength {
sub get_taxonomy_id {
my ($self, $dba) = @_;
+ $dba ||= $self->dba;
my $sql = 'SELECT meta_value FROM meta WHERE meta_key = "species.taxonomy_id"';
my $sth = $dba->dbc->db_handle->prepare($sql);
$sth->execute;
@@ -621,6 +832,7 @@ sub get_taxonomy_id {
sub get_species_scientific_name {
my ($self, $dba) = @_;
+ $dba ||= $self->dba;
my $sql = qq(
SELECT
meta_value
@@ -643,13 +855,38 @@ sub get_species_scientific_name {
return $species;
}
+=head2 species
+
+ Arg[1] : (optional) String $species - species name to set
+ Example : my $species = $support->species;
+ my $url = "http://vega.sanger.ac.uk/$species/";
+ Description : Getter/setter for species name (Genus_species). If not set, it's
+ determined from database's meta table
+ Return type : String - species name
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub species {
+ my $self = shift;
+ $self->{'_species'} = shift if (@_);
+ # get species name from database if not set
+ unless ($self->{'_species'}) {
+ $self->{'_species'} = join('_',
+ split(/ /, $self->get_species_scientific_name));
+ }
+ return $self->{'_species'};
+}
+
=head2 sort_chromosomes
- Arg[1] : Hashref $chr_hashref - Hashref with chr_name as keys
+ Arg[1] : (optional) Hashref $chr_hashref - Hashref with chr_name as keys
Example : my $chr = { '6-COX' => 1, '1' => 1, 'X' => 1 };
my @sorted = $support->sort_chromosomes($chr);
Description : Sorts chromosomes in an intuitive way (numerically, then
- alphabetically)
+ alphabetically). If no chromosome hashref is passed, it's
+ retrieve by calling $self->get_chrlength()
Return type : List - sorted chromosome names
Exceptions : thrown if no hashref is provided
Caller : general
@@ -658,6 +895,7 @@ sub get_species_scientific_name {
sub sort_chromosomes {
my ($self, $chr_hashref) = @_;
+ $chr_hashref = $self->get_chrlength unless ($chr_hashref);
throw("You have to pass a hashref of your chromosomes")
unless ($chr_hashref and ref($chr_hashref) eq 'HASH');
return (sort _by_chr_num keys %$chr_hashref);
@@ -705,11 +943,73 @@ sub _by_chr_num {
}
}
+=head2 split_chromosomes_by_size
+
+ Arg[1] : (optional) Int $cutoff - the cutoff in bp between small and
+ large chromosomes
+ Example : my $chr_slices = $support->split_chromosomes_by_size;
+ foreach my $block_size (keys %{ $chr_slices }) {
+ print "Chromosomes with blocksize $block_size: ";
+ print join(", ", map { $_->seq_region_name }
+ @{ $chr_slices->{$block_size} });
+ }
+ Description : Determines block sizes for storing DensityFeatures on
+ chromosomes, and return slices for each chromosome. The block
+ size is determined so that you have 150 bins for the smallest
+ chromosome over 5 Mb in length. For chromosomes smaller than 5
+ Mb, an additional smaller block size is used to yield 150 bins
+ for the overall smallest chromosome. This will result in
+ reasonable resolution for small chromosomes and high
+ performance for big ones.
+ Return type : Hashref (key: block size; value: Arrayref of chromosome
+ Bio::EnsEMBL::Slices)
+ Exceptions : none
+ Caller : density scripts
+
+=cut
+
+sub split_chromosomes_by_size {
+ my $self = shift;
+ my $cutoff = shift || 5000000;
+
+ my $slice_adaptor = $self->dba->get_SliceAdaptor;
+ my $top_slices;
+ if ($self->param('chromosomes')) {
+ foreach my $chr ($self->param('chromosomes')) {
+ push @{ $top_slices }, $slice_adaptor->fetch_by_region('chromosome', $chr);
+ }
+ } else {
+ $top_slices = $slice_adaptor->fetch_all("toplevel");
+ }
+
+ my ($big_chr, $small_chr, $min_big_chr, $min_small_chr);
+ foreach my $slice (@{ $top_slices }) {
+ if ($slice->length < $cutoff) {
+ if (! $min_small_chr or ($min_small_chr > $slice->length)) {
+ $min_small_chr = $slice->length;
+ }
+ # push small chromosomes onto $small_chr
+ push @{ $small_chr }, $slice;
+ }
+ if (! $min_big_chr or ($min_big_chr > $slice->length) && $slice->length > $cutoff) {
+ $min_big_chr = $slice->length;
+ }
+ # push _all_ chromosomes onto $big_chr
+ push @{ $big_chr }, $slice;
+ }
+
+ my $chr_slices;
+ $chr_slices->{int($min_big_chr/150)} = $big_chr if $min_big_chr;
+ $chr_slices->{int($min_small_chr/150)} = $small_chr if $min_small_chr;
+
+ return $chr_slices;
+}
+
=head2 log
Arg[1] : String $txt - the text to log
Arg[2] : Int $indent - indentation level for log message
- Example : my $log = $support->log_filehandle('>>');
+ Example : my $log = $support->log_filehandle;
$support->log('Log foo.\n', 1);
Description : Logs a message to the filehandle initialised by calling
$self->log_filehandle(). You can supply an indentation level
@@ -723,7 +1023,11 @@ sub _by_chr_num {
sub log {
my ($self, $txt, $indent) = @_;
$indent ||= 0;
- $txt = " "x$indent . $txt;
+
+ # strip off leading linebreaks so that indenting doesn't break
+ $txt =~ s/^(\n*)//;
+
+ $txt = $1." "x$indent . $txt;
my $fh = $self->{'_log_filehandle'};
throw("Unable to obtain log filehandle") unless $fh;
print $fh "$txt";
@@ -734,7 +1038,7 @@ sub log {
Arg[1] : String $txt - the warning text to log
Arg[2] : Int $indent - indentation level for log message
- Example : my $log = $support->log_filehandle('>>');
+ 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.
Return type : true on success
@@ -751,17 +1055,88 @@ sub log_warning {
return(1);
}
+=head2 log_error
+
+ Arg[1] : String $txt - the error text to log
+ Arg[2] : Int $indent - indentation level for log message
+ Example : my $log = $support->log_filehandle;
+ $support->log_error('Log foo.\n', 1);
+ Description : Logs a message via $self->log and exits the script.
+ Return type : none
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub log_error {
+ my ($self, $txt, $indent) = @_;
+ $txt = "ERROR: ".$txt;
+ $self->log($txt, $indent);
+ $self->log("Exiting.\n");
+ exit;
+}
+
+=head2 log_verbose
+
+ Arg[1] : String $txt - the warning text to log
+ Arg[2] : Int $indent - indentation level for log message
+ Example : my $log = $support->log_filehandle;
+ $support->log_verbose('Log this verbose message.\n', 1);
+ Description : Logs a message via $self->log if --verbose option was used
+ Return type : TRUE on success, FALSE if not verbose
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub log_verbose {
+ my ($self, $txt, $indent) = @_;
+
+ return(0) unless $self->param('verbose');
+
+ $self->log($txt, $indent);
+ return(1);
+}
+
+=head2 log_stamped
+
+ Arg[1] : String $txt - the warning text to log
+ Arg[2] : Int $indent - indentation level for log message
+ Example : my $log = $support->log_filehandle;
+ $support->log_stamped('Log this stamped message.\n', 1);
+ Description : Appends timestamp and memory usage to a message and logs it via
+ $self->log
+ Return type : TRUE on success
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub log_stamped {
+ my ($self, $txt, $indent) = @_;
+
+ # append timestamp and memory usage to log text
+ $txt =~ s/(\n*)$//;
+ $txt .= " ".$self->date_and_mem.$1;
+
+ $self->log($txt, $indent);
+ return(1);
+}
+
=head2 log_filehandle
- Arg[1] : String $mode - file access mode
- Example : my $log = $support->log_filehandle('>>');
+ Arg[1] : (optional) String $mode - file access mode
+ Example : my $log = $support->log_filehandle;
# print to the filehandle
print $log 'Lets start logging...\n';
# log via the wrapper $self->log()
$support->log('Another log message.\n');
Description : Returns a filehandle for logging (STDERR by default, logfile if
set from config or commandline). You can use the filehandle
- directly to print to, or use the smart wrapper $self->log()
+ directly to print to, or use the smart wrapper $self->log().
+ Logging mode (truncate or append) can be set by passing the
+ mode as an argument to log_filehandle(), or with the
+ --logappend commandline option (default: truncate)
Return type : Filehandle - the filehandle to log to
Exceptions : thrown if logfile can't be opened
Caller : general
@@ -770,7 +1145,8 @@ sub log_warning {
sub log_filehandle {
my ($self, $mode) = @_;
- $mode ||= ">";
+ $mode ||= '>';
+ $mode = '>>' if ($self->param('logappend'));
my $fh = \*STDERR;
if (my $logfile = $self->param('logfile')) {
if (my $logpath = $self->param('logpath')) {
@@ -783,13 +1159,44 @@ sub log_filehandle {
return $self->{'_log_filehandle'};
}
+=head2 filehandle
+
+ Arg[1] : String $mode - file access mode
+ Arg[2] : String $file - input or output file
+ Example : my $fh = $support->filehandle('>>', '/path/to/file');
+ # print to the filehandle
+ print $fh 'Your text goes here...\n';
+ Description : Returns a filehandle (*STDOUT for writing, *STDIN for reading
+ by default) to print to or read from.
+ Return type : Filehandle - the filehandle
+ Exceptions : thrown if file can't be opened
+ Caller : general
+
+=cut
+
+sub filehandle {
+ my ($self, $mode, $file) = @_;
+ $mode ||= ">";
+ my $fh;
+ if ($file) {
+ open($fh, "$mode", $file) or throw(
+ "Unable to open $file for writing: $!");
+ } elsif ($mode =~ />/) {
+ $fh = \*STDOUT;
+ } elsif ($mode =~ /</) {
+ $fh = \*STDIN;
+ }
+ return $fh;
+}
+
=head2 init_log
- Example : print LOG $support->init_log;
- Description : Returns some header information for a logfile. This includes
- script name, date, user running the script and parameters the
- script will be running with
- Return type : String - the log text
+ Example : $support->init_log;
+ Description : Opens a filehandle to the logfile and prints some header
+ information to this file. This includes script name, date, user
+ running the script and parameters the script will be running
+ with.
+ Return type : Filehandle - the log filehandle
Exceptions : none
Caller : general
@@ -798,27 +1205,33 @@ sub log_filehandle {
sub init_log {
my $self = shift;
+ # get a log filehandle
+ my $log = $self->log_filehandle;
+
# print script name, date, user who is running it
my $hostname = `hostname`;
chomp $hostname;
my $script = "$hostname:$Bin/$Script";
my $user = `whoami`;
chomp $user;
- my $txt = "Script: $script\nDate: ".$self->date."\nUser: $user\n";
+ $self->log("Script: $script\nDate: ".$self->date."\nUser: $user\n");
# print parameters the script is running with
- $txt .= "Parameters:\n\n";
- $txt .= $self->list_all_params;
+ $self->log("Parameters:\n\n");
+ $self->log($self->list_all_params);
- return $txt;
+ # remember start time
+ $self->{'_start_time'} = time;
+
+ return $log;
}
=head2 finish_log
- Example : print LOG $support->finish_log;
- Description : Return footer information to write to a logfile. This includes
- the number of logged warnings, timestamp and memory footprint.
- Return type : String - the log text
+ Example : $support->finish_log;
+ Description : Writes footer information to a logfile. This includes the
+ number of logged warnings, timestamp and memory footprint.
+ Return type : TRUE on success
Exceptions : none
Caller : general
@@ -826,8 +1239,18 @@ sub init_log {
sub finish_log {
my $self = shift;
- my $txt = "All done. ".$self->warnings." warnings. ".$self->date_and_mem."\n";
- return $txt;
+ $self->log("All done. ".$self->warnings." warnings. ");
+ if ($self->{'_start_time'}) {
+ $self->log("Runtime ");
+ my $diff = time - $self->{'_start_time'};
+ my $sec = $diff % 60;
+ $diff = ($diff - $sec) / 60;
+ my $min = $diff % 60;
+ my $hours = ($diff - $min) / 60;
+ $self->log("${hours}h ${min}min ${sec}sec ");
+ }
+ $self->log($self->date_and_mem."\n\n");
+ return(1);
}
=head2 date_and_mem
diff --git a/modules/Bio/EnsEMBL/Utils/SchemaConversion.pm b/modules/Bio/EnsEMBL/Utils/SchemaConversion.pm
index 1f2d8f564888812f5da16667a272c0dfa0f946dc..089914e2b5815fa0adf8588ceb2219d48b789788 100644
--- a/modules/Bio/EnsEMBL/Utils/SchemaConversion.pm
+++ b/modules/Bio/EnsEMBL/Utils/SchemaConversion.pm
@@ -48,7 +48,7 @@ use Data::Dumper;
Example : $conversion->Bio::EnsEMBL::Utils::SchemaConversion->new($serverroot);
Description : Constructor, including an instance of a Bio::EnsEMBL::Utils::ConversionSupport
- object. Parses input file
+ object. Parses input file and checks input with user
Return type : Bio::EnsEMBL::Utils::SchemaConversion object
Exceptions : thrown if $Siteroot not passed over
Caller : $Siteroot/utils/vega_schema_conversion
@@ -62,6 +62,42 @@ sub new {
bless ($self,$class);
$self->{config} = Bio::EnsEMBL::Utils::ConversionSupport->new($support);
$self->conv_support->parse_common_options;
+ $self->conv_support->parse_extra_options('do_vega_sc=s',
+ 'do_ens_sc=s',
+ 'source_db=s',
+ 'core_sql=s',
+ 'vega_sql=s',
+ 'patch_sql=s',
+ 'force=s',
+ 'do_features=s');
+
+ #check input and show help
+ $self->conv_usage() if ($self->conv_support->param("help"));
+ $self->conv_usage("configuration file needed") unless ($self->conv_support->param("conffile"));
+ $self->conv_usage("password for database access needed") unless ($self->conv_support->param("pass"));
+ $self->conv_usage("can only do conversion to ensembl OR Vega, not both") if ($self->conv_support->param('do_vega_sc') && $self->conv_support->param('do_ens_sc'));
+ $self->conv_usage("You need to do vega->veg or ensembl->vega conversion") unless ($self->conv_support->param('do_vega_sc') || $self->conv_support->param('do_ens_sc'));
+
+ # ask user to confirm parameters to proceed
+ $self->conv_support->allowed_params('conffile',
+ 'do_vega_sc',
+ 'do_ens_sc',
+ 'host',
+ 'port',
+ 'user',
+ 'pass',
+ 'source_db',
+ 'dbname',
+ 'force',
+ 'do_features',
+ 'verbose',
+ 'logpath',
+ 'logfile',
+ 'core_sql',
+ 'vega_sql',
+ 'patch_sql');
+ $self->conv_support->confirm_params;
+
my $siteroot = $self->conv_support->serverroot;
$self->conv_support->param('vega_sql',$siteroot.$self->conv_support->param('vega_sql'));
$self->conv_support->param('core_sql',$siteroot.$self->conv_support->param('core_sql'));
@@ -136,8 +172,9 @@ sub choose_conversion_type {
my $self = shift;
my $converter;
my $species;
+
$species = $self->species_alias($self->conv_support->param('source_db'));
- if ($self->conv_support->param('do_vega_schema_conversion')) {
+ if ($self->conv_support->param('do_vega_sc')) {
$species = "vega::".$species;
eval "require SeqStoreConverter::$species";
if($@) {
@@ -166,9 +203,9 @@ sub choose_conversion_type {
$converter = "SeqStoreConverter::$species"->new
( $self->conv_support->param('user'),
$self->conv_support->param('pass'),
- $self->conv_support->param('host'),
+ $self->conv_support->param('host').':'.$self->conv_support->param('port'),
$self->conv_support->param('source_db'),
- $self->conv_support->param('target_db'),
+ $self->conv_support->param('dbname'),
$self->conv_support->param('core_sql'),
$self->conv_support->param('vega_sql'),
$self->conv_support->param('force'),
@@ -200,8 +237,8 @@ sub do_conversion {
$self->conv_obj->create_assembly();
$self->conv_obj->create_attribs();
$self->conv_obj->set_top_level();
-
$self->conv_obj->transfer_dna();
+ $self->conv_obj->reset_gene_trans_tables();
$self->conv_obj->transfer_genes();
$self->conv_obj->transfer_prediction_transcripts();
@@ -214,7 +251,7 @@ sub do_conversion {
$self->conv_obj->copy_other_tables();
$self->conv_obj->copy_repeat_consensus();
$self->conv_obj->create_meta_coord();
- if ($self->conv_support->param('do_vega_schema_conversion')) {
+ if ($self->conv_support->param('do_vega_sc')) {
$self->conv_obj->copy_other_vega_tables();
$self->conv_obj->update_clone_info();
$self->conv_obj->remove_supercontigs();
@@ -235,7 +272,7 @@ sub do_conversion {
sub make_schema_up_to_date {
my $self = shift;
- $self->conv_obj->debug ("\n*** Patching schema to latest version ***\n");
+ $self->conv_obj->debug ("\nPatching schema to latest version\n");
my $user = $self->conv_obj->user;
my $pass = $self->conv_obj->password;
my $port = $self->conv_obj->port;
@@ -247,6 +284,7 @@ sub make_schema_up_to_date {
}
+
=head2 conv_usage
Example : $conversion->conv_usage("message")
@@ -265,27 +303,30 @@ sub conv_usage {
print STDERR <<EOF;
-usage: ./conversion_densities.pl <options>
+** Source and target databases must be on the same mysql instance
-options: -pass <password> the mysql user's password (required)
+usage: ./conversion_densities.pl <options>
- -conf <conf_file> configuration file (required):
+options: --conf <conf_file> configuration file (uses conf/Conversion.ini by default):
fields:
- do_vega_conversion (0 or 1)
- do_ensembl_conversion (0 or 1)
+ do_vega_sc (do vega conversion: 0 or 1)
+ do_ens_sc (do ensembl conversion: 0 or 1)
user (a mysql db user with read/write priveleges)
- host (plus port eg ecs3d:3307)
+ host (eg ecs3f)
+ port (eg 3310)
source_db (schema 19 source database)
- target_db (schema 20+ trget database)
- core_sql (location of ensembl schema creation script eg ensembl/sql/table.sql)
- vega_sql (location of creation script for additinoal vega tables eg ensembl/sql/vega_specific_tables.sql)
- patch_sql (location of schema patching script eg ensembl/sql/vega_latest_schema.sql)
- force (overwrite existing target database? 0 or 1)
- verbose (print out debug statements 0 or 1)
- do_features (0 or 1 - transfer dna- and protein-align features, for debugging)
-
- -help display this message
+ dbname (schema 20+ target database)
+ force (overwrite existing target database: 0 or 1)
+ verbose (print out debug statements: 0 or 1)
+ logpath (location of log file)
+ do_features (transfer dna- and protein-align features, for debugging: 0 or 1)
+ core_sql (location of ensembl schema creation script: ensembl/sql/table.sql)
+ vega_sql (location of creation script for additional vega tables: ensembl/sql/vega_specific_tables.sql)
+ patch_sql (location of schema patching script: ensembl/sql/vega_latest_schema.sql)
+
+ --log name of log_file
+ --help display this message
EOF
exit;
diff --git a/sql/patch_30_31.sql b/sql/patch_30_31.sql
index 96806cbe43b85698f6c1053e766fb5f6a34bf2b4..233a3ec4e7a45e99554ef7baa409b22faab4e8bb 100644
--- a/sql/patch_30_31.sql
+++ b/sql/patch_30_31.sql
@@ -21,6 +21,7 @@ ALTER TABLE transcript ADD description text;
UPDATE transcript t, xref x SET t.description = x.description WHERE t.display_xref_id = x.xref_id;
UPDATE transcript SET description=NULL WHERE description="";
+# usefull settings for the new tables
# usefull settings for the new tables
UPDATE gene SET biotype='protein_coding' WHERE biotype = 'ensembl';
@@ -29,6 +30,7 @@ UPDATE gene g, xref x, external_db ed SET g.confidence='KNOWN' WHERE g.display_x
UPDATE transcript t, xref x, external_db ed SET t.confidence='KNOWN' WHERE t.display_xref_id = x.xref_id and x.external_db_id = ed.external_db_id and t.display_xref_id != 0 and ed.status like 'KNOWN%';
# some vega specific stuff, shouldnt harm anybody else
+
UPDATE gene SET biotype='unclassified' WHERE biotype = 'Transcript';
UPDATE gene SET biotype='pseudogene' WHERE biotype = 'Pseudogene';
UPDATE gene SET biotype='protein_coding', confidence='NOVEL' WHERE biotype = 'Novel_CDS';
@@ -51,7 +53,6 @@ UPDATE transcript t, gene g SET t.biotype = g.biotype WHERE g.gene_id = t.gene_i
# new tables regulatory stuff and transcript supporting features
-
################################################################################
#
# Table structure for table 'regulatory_feature'