### Lastz Master Configuration Examples

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1DBAdaptor-members

Example configuration files for a 'LastzMaster' setup, likely for managing and coordinating Lastz alignment jobs. These examples cover different variations like core, conf, reg, and no-master setups, intended for legacy pipelines.

```perl
# Example: Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

# This configuration likely sets up parameters for a master Lastz job.

1;

# Example: Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

# This configuration likely sets up parameters for a non-master Lastz job.

1;

# ... other LastzMaster_conf examples follow similar structures ...

```

--------------------------------

### Example Configurations (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/BlastpWithReuse_8pm_source

Example configuration files demonstrating specific functionalities or setups within the Ensembl Compara pipeline.

```perl
# Bio/EnsEMBL/Compara/PipeConfig/Example/LoadMembersQfo_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Example/NoMasterProteinTrees_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Example/QfoProteinTrees_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Example/TuataraProteinTrees_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/CAFE_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/LastzMaster_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/LastzMasterConf_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/LastzMasterCore_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/LastzMasterReg_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/LastzNoMaster_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/LastzNoMasterConf_conf.pm
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/TBlatMaster_conf.pm
```

--------------------------------

### Legacy Example Lastz Master Configurations

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1GeneTrees_1_1CopyClusters-members

A series of configuration files starting with Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::Lastz* suggest example configurations for Lastz alignments, potentially involving a 'master' concept. These files serve as templates or examples for setting up Lastz pipelines in legacy or example contexts.

```perl
# Example configuration for Legacy Lastz Master
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

sub conf_assigner {
    return [
        {
            -class => 'Bio::EnsEMBL::Compara::RunnableDB::PairAligner::LastZ',
            - Tuhan => 'run_master_lastz',
            # Configuration details for master Lastz setup...
        }
    ];
}

```

--------------------------------

### Legacy Lastz Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1Families_1_1CopyUniprotData

Example configuration files for the Lastz alignment pipeline, demonstrating master and non-master configurations, including core and registry setups. These are part of the legacy examples.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

# Class implementation details would go here.
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

# Class implementation details would go here.
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

# Class implementation details would go here.
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

# Class implementation details would go here.
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

# Class implementation details would go here.
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

# Class implementation details would go here.
```

--------------------------------

### Lastz Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1PipeConfig_1_1LoadSpeciesTrees__conf-members

Example pipe configurations for Lastz alignments, demonstrating different master/configuration setups. These files likely serve as templates or examples for setting up Lastz pipelines.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;
# ... Example Lastz Master configuration ...

1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

use strict;
use warnings;
# ... Example Lastz MasterConf configuration ...

1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

use strict;
use warnings;
# ... Example Lastz MasterCore configuration ...

1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

use strict;
use warnings;
# ... Example Lastz MasterReg configuration ...

1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;
# ... Example Lastz NoMaster configuration ...

1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

use strict;
use warnings;
# ... Example Lastz NoMasterConf configuration ...

1;
```

--------------------------------

### Bio::EnsEMBL::Compara::PipeConfig::Example::NoMasterProteinTrees_conf - Example Configuration

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1PipeConfig_1_1Plants_1_1LoadMembers__conf-members

An example pipe configuration file for protein trees, specifically demonstrating a setup that does not involve a master database. Used for testing and illustrating pipeline setup.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Example::NoMasterProteinTrees_conf;

use strict;
use warnings;
use Bio::EnsEMBL::Hive::Process;

sub pipeline_wide_parameters {
  my ($self) = @_;
  my @params = (
    # Define parameters for the pipeline
  );
  return @params;
}

sub job_conditions {
  my ($self) = @_;
  my @conditions = (
    # Define job conditions
  );
  return @conditions;
}

1;
```

--------------------------------

### LastZ Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1ProteinTrees_1_1RAxML__bl-members

Example configuration files for LastZ Master, demonstrating various setups including master/non-master, core, and registry configurations. These are part of the legacy example configurations.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

# Example configuration for LastZ Master

```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

use strict;
use warnings;

# Example configuration for LastZ Master Conf

```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

use strict;
use warnings;

# Example configuration for LastZ Master Core

```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

use strict;
use warnings;

# Example configuration for LastZ Master Registry

```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

# Example configuration for LastZ without Master

```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

use strict;
use warnings;

# Example configuration for LastZ No Master Conf

```

--------------------------------

### Protein Trees Configuration - Example

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/PairAlignerCodingExonStats_8pm_source

Example configuration file for generating protein trees. This demonstrates the setup for phylogenetic tree construction in an example context.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Example::QfoProteinTrees_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::General;

sub as...

```

--------------------------------

### Install and Use TSSDistance VEP Plugin

Source: https://useast.ensembl.org/info/docs/tools/vep/script/vep_plugins

This example shows the installation and usage of the TSSDistance VEP plugin, which calculates the distance of variants from the transcription start site. It supports calculating distances in both upstream and downstream directions.

```bash
mv TSSDistance.pm ~/.vep/Plugins
./vep -i variations.vcf --plugin TSSDistance# Get both up and downstream distances:
./vep -i variations.vcf --plugin TSSDistance,both_direction=1
```

--------------------------------

### Install Ensembl VEP using INSTALL.pl script

Source: https://useast.ensembl.org/info/docs/tools/vep/script/vep_download

This command initiates the installation process for Ensembl VEP. It guides the user through downloading and configuring necessary components, including the Ensembl API, cache files, and FASTA files. Follow the on-screen prompts for a complete setup.

```bash
perl INSTALL.pl
```

--------------------------------

### LastzMaster Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1OrthologQM_1_1PrepareOrthologs

Example configuration files demonstrating different ways to set up Lastz Master runs, including configurations with and without a master database, and core/registry options.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Common;

sub schema_version {
    return 1;
}

sub lastz_master_conf {
    my $self = shift;
    my $params = shift || {};

    my $conf = {
        '-class' => 'Bio::EnsEMBL::Compara::RunnableDB::PairAligner::LastZ',
        'master_db' => 1, # Enable master database usage
        'method'    => 'lastz',
        # Other master-related parameters
    };

    %{$conf} = (%{$params} eq %{$conf});

    return $conf;
}

1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Common;

sub schema_version {
    return 1;
}

sub lastz_no_master_conf {
    my $self = shift;
    my $params = shift || {};

    my $conf = {
        '-class' => 'Bio::EnsEMBL::Compara::RunnableDB::PairAligner::LastZ',
        'master_db' => 0, # Disable master database usage
        'method'    => 'lastz',
        # Parameters for non-master runs
    };

    %{$conf} = (%{$params} eq %{$conf});

    return $conf;
}

1;
```

--------------------------------

### Legacy Lastz Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1GeneTrees_1_1QuickTreeBreak

Example configuration files for setting up LastZ alignment pipelines, specifically for master/non-master configurations, from legacy systems. These provide templates for LastZ pipeline setup.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

# Legacy example configuration for LastZ master pipeline
# ... master config details ...
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

# Legacy example configuration for LastZ master pipeline configuration
# ... master conf details ...
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

# Legacy example configuration for LastZ master core pipeline
# ... master core details ...
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

# Legacy example configuration for LastZ master registry pipeline
# ... master registry details ...
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

# Legacy example configuration for LastZ non-master pipeline
# ... non-master config details ...
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

# Legacy example configuration for LastZ non-master pipeline configuration
# ... non-master conf details ...
```

--------------------------------

### Get Absolute Start Coordinate on Sequence Region (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1PepDnaAlignFeature

This method is intended to return the absolute start coordinate of the feature on its sequence region. However, the provided code is incomplete and only includes the method signature and an example usage. It likely relies on internal attributes like 'hslice' and 'hstart'.

```perl
sub hseq_region_start {
  my $self  = shift;
  my $slice = $self->{'hslice'};

  # Incomplete implementation
  # return undef if (!$slice);
  # ... rest of the logic based on strand and hstart/hend ...
}
```

--------------------------------

### Legacy Lastz Master Configuration Examples

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1EpoExtended_1_1FindPairwiseMlssLocation-members

These configuration files provide examples for setting up Lastz pipelines within legacy Ensembl Compara versions. They cover different master/no-master scenarios and core configurations. Intended for users working with older pipeline setups.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Compara::PipeConfig::Standard_conf);


```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Compara::PipeConfig::Standard_conf);


```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Compara::PipeConfig::Standard_conf);


```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Compara::PipeConfig::Standard_conf);


```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Compara::PipeConfig::Standard_conf);


```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Compara::PipeConfig::Standard_conf);


```

--------------------------------

### Bio::EnsEMBL::Compara::PipeConfig::Example::NoMasterProteinTrees_conf

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1PipeConfig_1_1Vertebrates_1_1PigBreedsProteinTrees__conf

Configuration file for a pipe in the Ensembl Compara package, specifically for an example setup related to protein trees without a master database. This guides the execution of related analyses.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Example::NoMasterProteinTrees_conf;

use strict;
use warnings;
use base 'Bio::EnsEMBL::Pipeline::Config::StandardPipeline';

# Configuration details would be defined here...
```

--------------------------------

### Legacy Example Lastz Master Configuration

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1ObjectStore-members

Configuration files within the Legacy::Example directory for setting up Lastz jobs, including variations like 'LastzMaster', 'LastzNoMaster', and their associated configuration variants. These likely provide templates for different Lastz execution scenarios.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

sub default_options {
  my $self = shift;
  return (
    -master => 1,
    # ... Lastz options ...
  );
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

use strict;
use warnings;

sub default_options {
  my $self = shift;
  return (
    -master => 1,
    -config_file => 'master_config.cfg',
    # ... Lastz options ...
  );
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

use strict;
use warnings;

sub default_options {
  my $self = shift;
  return (
    -master => 1,
    -core_mode => 1,
    # ... Lastz options ...
  );
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

use strict;
use warnings;

sub default_options {
  my $self = shift;
  return (
    -master => 1,
    -registry_file => 'master_registry.pm',
    # ... Lastz options ...
  );
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

sub default_options {
  my $self = shift;
  return (
    -master => 0,
    # ... Lastz options ...
  );
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

use strict;
use warnings;

sub default_options {
  my $self = shift;
  return (
    -master => 0,
    -config_file => 'no_master_config.cfg',
    # ... Lastz options ...
  );
}

1;

```

--------------------------------

### Get Other Haplotypes

Source: https://useast.ensembl.org/info/docs/Doxygen/variation-api/TranscriptHaplotype_8pm_source

Get the partner TranscriptHaplotypes to this one. For example, get all CDSHaplotypes that translate to this ProteinHaplotype.

```APIDOC
## Get Other Haplotypes

### Description
Get the partner TranscriptHaplotypes to this one. For example, get all CDSHaplotypes that translate to this ProteinHaplotype.

### Method
GET

### Endpoint
`/websites/useast_ensembl_info/TranscriptHaplotype/other_haplotypes`

### Parameters
None

### Request Example
```json
{}
```

### Response
#### Success Response (200)
- **other_haplotypes** (array of TranscriptHaplotype) - An array of related TranscriptHaplotypes.

#### Response Example
```json
{
  "other_haplotypes": [
    {
      "id": "THABCDEF"
    }
  ]
}
```
```

--------------------------------

### Example Protein Tree Configuration for QFO

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1GeneSetQC_1_1StoreStatsAsTags

The `Example::QfoProteinTrees_conf` file provides an example configuration for generating protein trees, potentially using a specific method or dataset identified as 'QFO'. It serves as a template or demonstration for setting up protein tree pipelines.

```perl
use Bio::EnsEMBL::Compara::PipeConfig::Example::QfoProteinTrees_conf;
# This configuration file is an example for pipeline setup.
```

--------------------------------

### Get UCSC Coordinate Usage Flag (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/funcgen-api/classBio_1_1EnsEMBL_1_1Funcgen_1_1Parsers_1_1BaseImporter

Returns a boolean indicating whether UCSC coordinate usage is enabled for the object. This getter method checks the 'ucsc_coords' attribute. It's used in validation logic, as shown in the example where it conditionally increments a start position.

```Perl
sub ucsc_coords{
  return shift->{ucsc_coords};
}
```

--------------------------------

### Lastz Master Configuration - Legacy Example

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/RunnableDB_2GeneTrees_2GeneMemberHomologyStats_8pm

Configuration for the Lastz aligner when used in a master-slave setup, within a legacy example context. This setup is for pairwise sequence alignment.

```perl
# Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/LastzMaster_conf.pm
```

--------------------------------

### cdna_start

Source: https://useast.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1BaseTranscriptVariation

Gets or sets the start position of a variation on the transcript in cDNA coordinates. If the start position doesn't exist, it will calculate both start and end.

```APIDOC
## cdna_start

### Description
Getter/Setter for the start position of this variation on the transcript in cDNA coordinates. Will set both cdna_start and cdna_end if cdna_start does not exist.

### Method
Subroutine (Perl)

### Endpoint
N/A (Method within a class)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
* **$cdna_start** (int) - Optional - The cDNA start position to set.
* **$shifting_offset** (int) - Optional - An offset to apply during calculation.

### Request Example
```perl
# Get the cDNA start position
my $start = $tv->cdna_start();

# Set the cDNA start position
$tv->cdna_start(50);
```

### Response
#### Success Response (200)
* **int** - The cDNA start position.

#### Response Example
```json
50
```
```

--------------------------------

### QFO Protein Trees Configuration Example - Bio::EnsEMBL::Compara::PipeConfig::Example::QfoProteinTrees_conf

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1PipeConfig_1_1EPOAnchors__conf-members

An example configuration file for a protein trees pipeline, potentially related to 'QFO' (Query-Focused Orthologs). This serves as a template or demonstration for setting up such a pipeline. It likely defines basic parameters and steps.

```perl
# Example pipe configuration for QFO ProteinTrees

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf;

# Example configuration
my $pipe_conf = Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf->new(
  -name    => "ExampleQfoProteinTrees",
  -species_sets => ["example_set"],
  # ... example parameters ...
);

# ... example steps ...

1;
```

--------------------------------

### Configuration for Loading Members QFO Example (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1PairAligner_1_1ImportNets

An example configuration file for loading members using the QFO (Quick Format Output) method within the Ensembl Compara pipeline. This is likely for testing or specific data formats.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Example::LoadMembersQfo_conf;

# Example configuration for loading members using QFO

1;
```

--------------------------------

### Get Feature Start Position

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1AssemblyExceptionFeature

Getter/Setter for the start position of the feature. This method is intended to return an integer representing the start coordinate.

```Perl
sub start {
  my ( $self, $start ) = @_;

  if ( defined $start ) {
    $self->{'start'} = $start;
  }

  return $self->{'start'};
}

```

--------------------------------

### Get/Set Exon Attribute (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1AlignSlice_1_1Exon

Provides a method to get or set the 'exon' attribute of an AlignSlice::Exon object. When getting the exon, it returns the starting position on the AlignSlice, potentially differing from the original exon's start position. The original start can be accessed via SUPER::start() or original_start().

```perl
sub exon {
  my ($self, $exon) = @__;

  if (defined($exon)) {
    $self->{'exon'} = $exon;

```

--------------------------------

### Legacy Lastz Master Configuration Examples

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1PipeConfig_1_1PairAligner__conf

Example configuration files for the Lastz Master pipeline in a legacy format. These demonstrate different setups for Lastz, including core, conf, and registry configurations.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::General;

sub default_options {
    my ($self) = @_;
    my $options = $self->SUPER::default_options();
    $options->{'master_mode'} = 1;
    return $options;
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::General;

sub default_options {
    my ($self) = @_;
    my $options = $self->SUPER::default_options();
    $options->{'master_mode'} = 1;
    $options->{'config_only'} = 1;
    return $options;
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::General;

sub default_options {
    my ($self) = @_;
    my $options = $self->SUPER::default_options();
    $options->{'master_mode'} = 1;
    $options->{'core_only'} = 1;
    return $options;
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::General;

sub default_options {
    my ($self) = @_;
    my $options = $self->SUPER::default_options();
    $options->{'master_mode'} = 1;
    $options->{'registry_only'} = 1;
    return $options;
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::General;

sub default_options {
    my ($self) = @_;
    my $options = $self->SUPER::default_options();
    $options->{'master_mode'} = 0;
    return $options;
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::General;

sub default_options {
    my ($self) = @_;
    my $options = $self->SUPER::default_options();
    $options->{'master_mode'} = 0;
    $options->{'config_only'} = 1;
    return $options;
}

1;

```

--------------------------------

### Example QFO Protein Tree Pipeline Configuration

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1FamilyAdaptor-members

An example configuration file for the ProteinTrees pipeline, potentially using a 'QFO' (Query From Orthologs) approach. This serves as a template or demonstration for setting up such pipelines.

```Perl
use Bio::EnsEMBL::Compara::PipeConfig::Example::QfoProteinTrees_conf;
```

--------------------------------

### Perl: Run command with example parameter setup and Ensembl Registry loading

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1AncestralAllelesForIndels_1_1RunAncestralAllelesCompleteFork

Executes a command, with optional setup for example parameters and loading the Ensembl Registry. When the 'example' parameter is defined, it sets default species, region, and path parameters, loads the Ensembl registry, and configures the compara URL. It allows disabling write operations.

```perl
sub run_cmd {
    my ($self) = @_;

    
    my $registry = 'Bio::EnsEMBL::Registry';

    my $output; #hash to contain all the variables I want to write to the database

    #=====================================================================
    # Example parameters (just to test the code or extract example alignments)
    #=====================================================================
    if ($self->param_is_defined('example')) {

        # Sets an example query region (human:6:133078660-133078700)
        $self->param('ref_species', 'homo_sapiens') if (!$self->param_is_defined('ref_species'));
        $self->param('seq_region', '6') if (!$self->param_is_defined('seq_region'));
        $self->param('seq_region_start', '133078660') if (!$self->param_is_defined('seq_region_start'));
        $self->param('seq_region_end', '133078700') if (!$self->param_is_defined('seq_region_end'));

        # Work dir set to current directory and sub_dir ignored.
        $self->param('work_dir', '.') if (!$self->param_is_defined('work_dir'));
        $self->param('sub_dir', '') if (!$self->param_is_defined('sub_dir'));
        
        # Connect to the public databases. The registry is required to connect to all the primates and the compara_url is required by the module)
        use Bio::EnsEMBL::Registry;
        Bio::EnsEMBL::Registry->load_registry_from_url('mysql://anonymous@ensembldb.ensembl.org/');
        use Bio::EnsEMBL::ApiVersion;
        $self->param('compara_url', 'mysql://anonymous@ensembldb.ensembl.org/ensembl_compara_'.software_version()) if (!$self->param_is_defined('compara_url'));
        
        # This enable the output of the Ortheus alignments
        $self->param('verbose', '1') if (!$self->param_is_defined('verbose'));
        
        # Disable the write_output step, which is meant to store the stats on the DB.
        $self->execute_writes(0);
    }
    #=====================================================================

    my $ref_species = $self->param('ref_species');
    my $seq_region = $self->param('seq_region');

```

--------------------------------

### QFO Protein Trees Example Configuration - Bio::EnsEMBL::Compara::PipeConfig::Example::QfoProteinTrees_conf

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1SystemCommands-members

An example configuration file for a protein tree pipeline, specifically for the QFO (Query Finding Online) system. This serves as a template or demonstration for setting up similar pipelines. It requires Ensembl core libraries.

```Perl
use Bio::EnsEMBL::Compara::PipeConfig::Example::QfoProteinTrees_conf;
# This module provides configuration settings for an example pipeline.
```

--------------------------------

### Set/Get Start Position in Bio::EnsEMBL::Feature

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1ProteinFeature

This method is used to get or set the start position of a feature relative to the start of its slice. It accepts an optional integer argument for the start position. The start position is 1-based and inclusive.

```perl
sub start {
  my ( $self, $value ) = @_; 
  if ( defined($value) ) {
    $self->{'start'} = $value;
  }
  return $self->{'start'};
}
```

--------------------------------

### Legacy Lastz Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1ProteinTrees_1_1CDHit-members

Example configurations for legacy Lastz pipelines, demonstrating different setups for master/non-master configurations. These provide templates for setting up Lastz jobs in older pipeline frameworks.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

# ... legacy Lastz master configuration example ...

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

# ... legacy Lastz master conf example ...

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

# ... legacy Lastz master core configuration example ...

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

# ... legacy Lastz master registry configuration example ...

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

# ... legacy Lastz no-master configuration example ...

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

# ... legacy Lastz no-master conf example ...

1;
```

--------------------------------

### Get Cluster Start Coordinate

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/GeneCluster_8pm_source

The `start` method retrieves the starting coordinate of the genomic range covered by the GeneCluster. This coordinate is determined by the start of the leftmost exon, ordered by their start positions, irrespective of the strand. The method also allows for setting the start coordinate.

```perl
# method to get the start of the cluster, which we take to be the left_most exon_coordinate
# i.e. the start coordinate of the first exon ordered as { $a->start <=> $b->start }, regardless of the strand

sub start {
  my ($self, $start) = @_ ;

  if ($start) {
    # ... (code to set start) ...
  }
  # ... (code to get start) ...
}

```

--------------------------------

### Get Bound Start Coordinate (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/funcgen-api/RegulatoryFeature_8pm_source

Calculates and retrieves the 5' most start value of the underlying attribute features in local coordinates. It uses the feature's start position and its bound start length.

```Perl
sub bound_start { return $_[0]->start - $_[0]->bound_start_length; }
```

--------------------------------

### Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1FunnelCheck

Legacy example configuration for a Lastz master pipeline. This configuration file provides an example setup for a Lastz alignment pipeline, likely for demonstration or older versions.

```perl
# Legacy example configuration for Lastz Master Pipeline

my $pipeline_options = {
  'analysis' => 'lastz_master',
  'genome_db_ids' => [1, 2, 3], # Example genome DB IDs
  'lastz_options' => [
    '--step=1000',
    '--chain'
  ],
  # ... other legacy options ...
};

$pipeline_options;

```

--------------------------------

### Get SeqEdit Start Position

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1SeqEdit

Retrieves the start position of a sequence edit. This method can also optionally set the start position if a value is provided.

```perl
sub start {
  my $self = shift;
  $self->{'start'} = shift if(@_);
  return $self->{'start'};
}
```

--------------------------------

### Legacy Lastz Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1GeneMemberAdaptor

Example configuration files for Lastz alignments, focusing on master/non-master configurations within legacy Ensembl Compara pipelines. These illustrate different ways to set up Lastz jobs.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

sub fetch_config {
  my ($self) = @_;
  return { # ... Lastz master config ... };
}

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

sub fetch_config {
  my ($self) = @_;
  return { # ... Lastz master conf config ... };
}

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

sub fetch_config {
  my ($self) = @_;
  return { # ... Lastz master core config ... };
}

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

sub fetch_config {
  my ($self) = @_;
  return { # ... Lastz master registry config ... };
}

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

sub fetch_config {
  my ($self) = @_;
  return { # ... Lastz no master config ... };
}

1;
```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

sub fetch_config {
  my ($self) = @_;
  return { # ... Lastz no master conf config ... };
}

1;
```

--------------------------------

### Legacy Lastz Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Production_1_1EPOanchors_1_1HMMer_1_1LoadConsEles

Example configuration files from the legacy directory for setting up Lastz master pipelines. These configurations illustrate different ways to manage Lastz master processes, including with and without master cores and registries.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

# Legacy example for Lastz master configuration

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

use strict;
use warnings;

# Legacy example for Lastz master configuration with conf

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

use strict;
use warnings;

# Legacy example for Lastz master configuration with core

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

use strict;
use warnings;

# Legacy example for Lastz master configuration with registry

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

# Legacy example for Lastz configuration without master

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

use strict;
use warnings;

# Legacy example for Lastz configuration without master and with conf

```

--------------------------------

### Set and Get Start Coordinate in Perl

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/ExonCluster_8pm_source

The 'start' subroutine allows setting and retrieving the start coordinate of the exon cluster. It validates that the provided start value is an integer before assigning it to the internal '_start' property.

```perl
sub start{
  my ($self,$start) = @_; 
  if ($start){
    $self->throw( "$start is not an integer") unless $start =~/^[-+]?\d+$/;
    $self->{'_start'} = $start;
  }
  return $self->{'_start'};
}
```

--------------------------------

### Get/Set Translation Start Position (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/variation-api/BaseTranscriptVariation_8pm_source

Gets or sets the start position of a variation on a transcript in peptide coordinates. If the translation start is not provided, it calculates both the translation start and end based on transcript translation coordinates. Returns the translation start coordinate.

```perl
sub translation_start {
    my ($self, $translation_start, $shifting_offset) = @_;
    
    $self->{translation_start} = $translation_start if defined $translation_start;

    unless (exists $self->{translation_start}) {
        my $translation_coords = $self->translation_coords($shifting_offset);
        
        my ($first, $last) = ($translation_coords->[0], $translation_coords->[-1]);
        
        $self->{translation_start} = $first->isa('Bio::EnsEMBL::Mapper::Gap') ? undef : $first->start;
        $self->{translation_end}   = $last->isa('Bio::EnsEMBL::Mapper::Gap') ? undef : $last->end;
    }

    return $self->{translation_start};
}
```

--------------------------------

### Legacy LASTZ Master Configuration Examples

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1PipeConfig_1_1OrthologQM__GeneOrderConservation__conf

Example configuration files for setting up LASTZ alignment pipelines in a legacy context, specifically demonstrating 'LastzMaster' configurations. These likely showcase different ways to manage master/slave processes or define core parameters for LASTZ runs.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

sub get_config {
    return { 'master_config' => 'path/to/master_config.pm' };
}
1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

sub get_config {
    return { 'core_config' => 'path/to/core_config.pm' };
}
1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

sub get_config {
    return { 'master_options' => '--threads 8' };
}
1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

sub get_config {
    return { 'registry_file' => 'path/to/registry.pm' };
}
1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

sub get_config {
    return { 'no_master' => 1 };
}
1;
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

sub get_config {
    return { 'standalone' => 1 };
}
1;
```

--------------------------------

### Legacy Lastz Master Configuration Examples (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1PipeConfig_1_1TBlat__conf

A set of example configuration files for Lastz alignment, specifically demonstrating different master/no-master configurations and their associated core and registration settings. These are useful for understanding Lastz pipeline setups in legacy contexts.

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

# Module content would go here
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

# Module content would go here
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

# Module content would go here
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

# Module content would go here
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

# Module content would go here
```

```perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

# Module content would go here
```

--------------------------------

### Get Feature Start Position

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1PredictionTranscript

Retrieves the start position of a feature relative to the start of the slice it resides on. This is an inherited method from the Bio::EnsEMBL::Feature class.

```perl
# Example usage:
# $start = $feat->start()

```

--------------------------------

### Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster Configurations

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1RunnableDB_1_1ProteinTrees_1_1TrimAl

Example configurations for the LastzMaster pipeline within the legacy examples directory. These demonstrate different setups for managing LASTZ jobs, with and without a master configuration.

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMaster_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMaster;

sub Job_conf {
  my $self = shift;
  # Example configuration for LastzMaster
  return Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMaster->new(@_);
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterConf_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMasterConf;

sub Job_conf {
  my $self = shift;
  # Example configuration for LastzMaster with a config file
  return Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMasterConf->new(@_);
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterCore_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMasterCore;

sub Job_conf {
  my $self = shift;
  # Example core configuration for LastzMaster
  return Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMasterCore->new(@_);
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzMasterReg_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMasterReg;

sub Job_conf {
  my $self = shift;
  # Example registry configuration for LastzMaster
  return Bio::EnsEMBL::Compara::PipeConfig::Std::LastzMasterReg->new(@_);
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMaster_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Std::LastzNoMaster;

sub Job_conf {
  my $self = shift;
  # Example configuration for LASTZ without a master
  return Bio::EnsEMBL::Compara::PipeConfig::Std::LastzNoMaster->new(@_);
}

1;

```

```Perl
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::LastzNoMasterConf_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Std::LastzNoMasterConf;

sub Job_conf {
  my $self = shift;
  # Example configuration for LASTZ without a master, using a config file
  return Bio::EnsEMBL::Compara::PipeConfig::Std::LastzNoMasterConf->new(@_);
}

1;

```