Ensembl Variant Effect Predictor

https://useast.ensembl.org/info/docs/
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Ensembl Variant Effect Predictor (VEP) is a powerful and configurable command-line tool for...
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### 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;
```

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

### fetch_input

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Hive_1_1RunnableDB_1_1HivePmatch

Fetches input sequence, sets up the database connection, and creates a Pmatch runnable.

```APIDOC
## POST /websites/useast_ensembl_info/fetch_input

### Description
Fetches input sequence, sets up the database connection, and creates a Pmatch runnable.

### Method
POST

### Endpoint
/websites/useast_ensembl_info/fetch_input

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
* **runnable** (Bio::EnsEMBL::Analysis::Runnable::Pmatch) - The created Pmatch runnable object.

#### Response Example
{
  "runnable": "Bio::EnsEMBL::Analysis::Runnable::Pmatch_instance"
}
```

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

### 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
```

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

### Database Initialization and Setup Scripts

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/ExonerateCloneEnds_8pm

Scripts for initializing new databases, creating necessary tables, and setting up pipeline components.

```Perl
use strict;
use warnings;

package Analysis::Hive::RunnableDB::HiveCreateDatabase;

use base qw(Analysis::Hive::RunnableDB::RunnableDBBase);

sub run {
    my ($self) = @_;
    # ... implementation for creating a database ...
    $self->log_message("Database created.");
    return 0;
}

1;
```

```Perl
use strict;
use warnings;

package Analysis::Hive::RunnableDB::HiveMetaPipelineInit;

use base qw(Analysis::Hive::RunnableDB::RunnableDBBase);

sub run {
    my ($self) = @_;
    # ... implementation for initializing meta pipeline ...
    $self->log_message("Meta pipeline initialized.");
    return 0;
}

1;
```

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

### 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 ...
}
```

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

### Initialize Configuration (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Tools_1_1ConfigUtils

Initializes a new configuration object. It can take a configuration module and an example flag as arguments. It also parses the configuration file using PPI::Document.

```perl
sub new {
  my ($class,@args) = @_;
  my $self = bless {},$class;

  my ($config_module, $is_example) = rearrange (['CONFIG', 'IS_EXAMPLE'], @args);

  $self->config_module($config_module, $is_example) if $config_module;
  $self->{_doc}= PPI::Document->new($self->file($is_example));
  return $self;
}

```

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

### 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...
```

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

### POST /websites/useast_ensembl_info/new

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Runnable_1_1ExonerateCloneEnds

Initializes a new instance of the Bio::EnsEMBL::Analysis::Runnable::ExonerateCloneEnds class.

```APIDOC
## POST /websites/useast_ensembl_info/new

### Description
Initializes a new instance of the Bio::EnsEMBL::Analysis::Runnable::ExonerateCloneEnds class.

### Method
POST

### Endpoint
/websites/useast_ensembl_info/new

### Parameters
#### Request Body
- **args** (object) - Optional - Arguments to pass to the constructor.

### Request Example
```json
{
  "args": {}
}
```

### Response
#### Success Response (200)
- **instance** (object) - A new instance of the ExonerateCloneEnds runnable.

#### Response Example
```json
{
  "instance": {}
}
```
```

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

### CloneEndsLinking Synopsis and Usage Example

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1RunnableDB_1_1CloneEndsLinking

Provides a synopsis and a concrete example of how to instantiate and use the Bio::EnsEMBL::Analysis::RunnableDB::CloneEndsLinking class. It demonstrates setting up the object with database and analysis information, fetching input, running the alignment process, and writing the output to the database.

```perl
my $clonemap = \
  Bio::EnsEMBL::Analysis::RunnableDB::CloneEndsLinking->new(
    -db         => $refdb,
    -analysis   => $analysis_obj,
    -database   => $EST_GENOMIC,
  );

$clonemap->fetch_input();
$clonemap->run();
$clonemap->write_output(); #writes to DB
```

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

### 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"
    }
  ]
}
```
```

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

### Bio::EnsEMBL::Analysis::Hive::RunnableDB::HiveBaseRunnableDB::setup_fasta_db

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Hive_1_1RunnableDB_1_1HiveBaseRunnableDB

Sets up the FASTA database for a Hive analysis.

```APIDOC
## Bio::EnsEMBL::Analysis::Hive::RunnableDB::HiveBaseRunnableDB::setup_fasta_db

### Description
Sets up the FASTA database for a Hive analysis.

### Method
`setup_fasta_db`

### Endpoint
None (This is a method call on an existing object)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```perl
$hive_db->setup_fasta_db();
```

### Response
#### Success Response (200)
Void (This method performs an action and does not return a value).

#### Response Example
```json
null
```
```

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

### 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 ...

```

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

### 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};
}
```

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

### 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.
```

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

### Synopsis for Bio::EnsEMBL::Analysis::RunnableDB::BlastRNASeqPep

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1RunnableDB_1_1BlastRNASeqPep

This synopsis demonstrates how to instantiate and use the Bio::EnsEMBL::Analysis::RunnableDB::BlastRNASeqPep object. It shows the creation of a new object with database, input ID, and analysis details, followed by fetching input, running the analysis, and retrieving the output.

```perl
my $db          = Bio::EnsEMBL::DBAdaptor->new($locator);
my $btpep     = Bio::EnsEMBL::Analysis::RunnableDB::BlastRNASeqPep->new ( 
                                                    -dbobj      => $db,
                                        -input_id   => $input_id
                                                    -analysis   => $analysis );

$btpep->fetch_input();
$btpep->run();
$btpep->output();

```

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

### 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
```
```

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

### Perl: Create BlastExonerate Runnable

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1RunnableDB_1_1Finished_1_1BlastExonerate

Initializes a Bio::EnsEMBL::Analysis::Runnable::Finished::BlastExonerate object with masked slice data and analysis configuration. This is a core setup step for running blast exonerate analyses.

```perl
my $runnable = Bio::EnsEMBL::Analysis::Runnable::Finished::BlastExonerate->new(
    '-hard_masked'    => $hard_masked_slice,
    '-soft_masked'    => $soft_masked_slice,
    '-analysis' => $self->analysis,
);
$self->runnable($runnable);
return 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'};
}

```

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

### Set Up Analysis with Database Backup Requirement

Source: https://useast.ensembl.org/info/docs/Doxygen/production-api/classBio_1_1EnsEMBL_1_1Production_1_1Pipeline_1_1PipeConfig_1_1RNAGeneXref__conf

Configures the 'AnalysisSetup' module, which requires a database backup to be present. It specifies the path to the backup file and indicates whether to delete existing data. It also includes a lookup for production-related information and links specific tables for dependent operations.

```perl
{
      -logic_name        => 'AnalysisSetup',
      -module            => 'Bio::EnsEMBL::Production::Pipeline::Common::AnalysisSetup',
      -max_retry_count   => 0,
      -analysis_capacity => 20,
      -parameters        => {
                              db_backup_required => 1,
                              db_backup_file     => catdir($self->o('pipeline_dir'), '#dbname#', 'pre_pipeline_bkp.sql.gz'),
                              delete_existing    => $self->o('delete_existing'),
                              linked_tables      => ['object_xref'],
                              production_lookup  => 1,
                            },
    }
```

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

### 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;

```

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

### 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;
```

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

### Exonerate2Genes Fetch Input Setup in Perl

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/HiveExonerate2Genes_8pm_source

This Perl code outlines the initial steps within the 'fetch_input' method of Exonerate2Genes. It sets up the FASTA database, retrieves a database adaptor for the 'target_db', and prepares for setting up the analysis and input query sequences.

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

  $self->setup_fasta_db;
  my $dba = $self->get_database_by_name('target_db');
  $self->hrdb_set_con($dba,'target_db');


  ##########################################
  # set up the target (genome)
  ##########################################

  $self->create_analysis;
  my @db_files;

  ##########################################
  # set up the query (est/cDNA/protein)
  ##########################################
  my $iid_type = $self->param('iid_type');
  my ($querys, $query_file,$chunk_number,$chunk_total, $query_seq);
  unless($iid_type) { 

```

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

### 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');

```

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

### Setup Fasta Database

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Hive_1_1RunnableDB_1_1HiveGenerateBestTargettedIndex

Configures the system to use a FASTA database. This is a public method.

```APIDOC
## PUBLIC setup_fasta_db ()

### Description
Initializes or configures the system to work with a FASTA formatted database. This public method is essential for processing sequence data in FASTA format.

### Method
PUBLIC

### Endpoint
N/A (Internal method)

### Parameters
None

### Request Example
None

### Response
#### Success Response (Void)
This method performs setup operations and does not return a value.

#### Response Example
None
```

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

### 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'};
}
```

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

### Example Usage of Bio::EnsEMBL::Analysis::RunnableDB::Infernal

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/HiveCMSearch_8pm_source

Demonstrates how to instantiate and use the Bio::EnsEMBL::Analysis::RunnableDB::Infernal module. This includes setting up the database adaptor, input ID, and analysis object, followed by the typical workflow of fetching input, running the analysis, and writing the output.

```perl
my $runnableDB = Bio::EnsEMBL::Analysis::RunnableDB::Infernal->new(
          -db       => $db_adaptor,
          -input_id => $flag_id,
          -analysis => $analysis,
                );
$runnabledb->fetch_input();
$runnabledb->run();
$runnabledb->write_output();
```

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

### 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; }
```

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

### 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;
```

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

### 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'};
}
```

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

### 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.
```

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

### RunnableDB: Setup Fasta Database

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Hive_1_1RunnableDB_1_1HiveGeneBuilder

Sets up the fasta database using Bio::EnsEMBL::Analysis::Tools::Utilities::setup_fasta_db() if the 'use_genome_flatfile' parameter is true.

```APIDOC
## POST /setup_fasta_db

### Description
Sets up the fasta database for retrieving genomic sequence from a fasta file. This method should preferably be called before any DBAdaptor calls. It relies on the 'use_genome_flatfile' parameter being set.

### Method
POST

### Endpoint
`/setup_fasta_db`

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
- **use_genome_flatfile** (Boolean) - Optional - If true, initiates the fasta database setup.

### Request Example
```json
{
  "use_genome_flatfile": true
}
```

### Response
#### Success Response (200)
- **status** (String) - Indicates the success of the operation.

#### Response Example
```json
{
  "status": "Fasta database setup initiated."
}
```
```

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

### Analysis Setup Configuration (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/production-api/classBio_1_1EnsEMBL_1_1Production_1_1Pipeline_1_1PipeConfig_1_1GeneNameDescProjection__conf

Sets up the parameters for subsequent analyses, including logic names, production lookup flags, deletion flags, and database backup file paths. It utilizes the Common::AnalysisSetup module and specifies resource constraints like '2GB' rc_name.

```perl
{
      -logic_name        => 'AnalysisSetup',
      -module            => 'Bio::EnsEMBL::Production::Pipeline::Common::AnalysisSetup',
      -analysis_capacity => 5,
      -max_retry_count   => 0,
      -parameters        => {
                              logic_name => $self->o('logic_name'),
                              production_lookup  => 1,
                              delete_existing => 1,
                              db_backup_file => catdir('#pipeline_dir#', '#config_type#', '#dbname#_bkp.sql.gz'),
                            },
      -rc_name           => '2GB',
    }
```

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

### 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};
}
```

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

### Database Initialization and Setup Modules

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/Bam2BigWig__conf_8pm_source

These modules are responsible for initializing and setting up databases, including creating new databases, directories, and potentially loading initial components or patches. They ensure the underlying data infrastructure is ready for analysis pipelines. Dependencies include database access and file system operations.

```Perl
package Analysis::Hive::RunnableDB::HiveCreateDatabase;
package Analysis::Hive::RunnableDB::HiveCreateDirectories;
package Analysis::Hive::RunnableDB::HiveLoadAssemblyComponents;
package Analysis::Hive::RunnableDB::HiveLoadPatches;
package Analysis::Hive::RunnableDB::HiveMetaPipelineInit;
```

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

### HiveBaseRunnableDB::setup_fasta_db

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Hive_1_1RunnableDB_1_1HiveWGA2GenesDirect

Sets up the FASTA database for sequence retrieval. If 'use_genome_flatfile' parameter is true, it calls the utility function to set up the FASTA database.

```APIDOC
## Bio::EnsEMBL::Analysis::Hive::RunnableDB::HiveBaseRunnableDB::setup_fasta_db

### Description
Sets up the FASTA database for sequence retrieval. If 'use_genome_flatfile' parameter is true, it calls the utility function to set up the FASTA database.

### Method
SUBROUTINE

### Endpoint
N/A

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
None

#### Response Example
None

### Notes
This method is inherited and intended to be called before any DBAdaptor calls.
```

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

### 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()

```

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

### Configure AnalysisSetup for Pipeline Initialization

Source: https://useast.ensembl.org/info/docs/Doxygen/production-api/classBio_1_1EnsEMBL_1_1Production_1_1Pipeline_1_1PipeConfig_1_1GPAD__conf

Sets up the AnalysisSetup module, which is responsible for initializing analysis stages. It takes parameters such as delete_existing, production_lookup, and program details, and does not require a database backup.

```perl
-logic_name        => 'AnalysisSetup',
-module            => 'Bio::EnsEMBL::Production::Pipeline::Common::AnalysisSetup',
-max_retry_count   => 0,
-analysis_capacity => 20,
-parameters        => {
    db_backup_required => 0,
    delete_existing    => $self->o('delete_existing'),
    production_lookup  => $self->o('production_lookup'),
    logic_name         => $self->o('logic_name'),
    db                 => $self->o('db'),
    program            => $self->o('program'),
    linked_tables      => $self->o('linked_tables')
}

```

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

### 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...

```

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

### Get Genomic Start Position of Translation (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation

Retrieves the start position of a translation in genomic coordinates on the forward strand. This method caches the result. It relies on the translation's start exon and its own start position.

```perl
sub genomic_start {
    my $self = shift;

    if ( !exists $self->{'genomic_start'} ) {
        if ( $self->start_Exon()->strand() >= 0 ) {
            $self->{'genomic_start'} =
              $self->start_Exon()->start() + ( $self->start() - 1 );
        } else {
            $self->{'genomic_start'} =
              $self->end_Exon()->end() - ( $self->end() - 1 );
        }
    }

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

```

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

### Production Table Population and Assembly Setup

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/CloneEndsLinking_8pm

Scripts for populating production tables and setting up the assembly pipeline, including defining toplevel sequences and synonyms. These scripts ensure the database is ready for annotation and analysis.

```Perl
package Analysis::Hive::RunnableDB::HiveAssemblyLoading::HivePopulateProductionTables;

use strict;
use warnings;

sub run {
  my ($self) = @_;
  # ... implementation details ...
}

1;

```

```Perl
package Analysis::Hive::RunnableDB::HiveAssemblyLoading::HiveSetAndCheckToplevel;

use strict;
use warnings;

sub run {
  my ($self) = @_;
  # ... implementation details ...
}

1;

```

```Perl
package Analysis::Hive::RunnableDB::HiveAssemblyLoading::HiveSetMetaAndSeqRegionSynonym;

use strict;
use warnings;

sub run {
  my ($self) = @_;
  # ... implementation details ...
}

1;

```

```Perl
package Analysis::Hive::RunnableDB::HiveAssemblyLoading::HiveSetupAssemblyPipeline;

use strict;
use warnings;

sub run {
  my ($self) = @_;
  # ... implementation details ...
}

1;

```

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

### ExonerateCloneEnds Class Synopsis

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1RunnableDB_1_1ExonerateCloneEnds

Demonstrates how to instantiate and use the ExonerateCloneEnds class. It outlines the required parameters for initialization and the sequence of methods to call for processing clone sequences.

```perl
my $clone = 
  Bio::EnsEMBL::Analysis::RunnableDB::ExonerateCloneEnds->new(
    -db         => $refdb,
    -analysis   => $analysis_obj,
    -database   => $EST_GENOMIC,
  );

$clone->fetch_input();
$clone->run();
$clone->write_output(); #writes to DB

```

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

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

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DnaPepAlignFeature

Gets or sets the start position of a feature relative to the start of its associated slice. Coordinates start at 1 and are inclusive. Negative values or values exceeding slice length are permitted, but start must be <= end.

```perl
sub start {
  my $self = shift;
  
  # Getter/Setter logic would typically be here
  # Example: if(@_) { $self->{'start'} = shift; }
  # return $self->{'start'};
  
  # Placeholder for actual implementation
  return undef; 
}
```

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

### GET /feature/end

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1SimpleFeature

Retrieves or sets the end position of a feature relative to the start of its slice. Coordinates start at 1 and are inclusive. End must be greater than or equal to start.

```APIDOC
## GET /feature/end

### Description
Getter/Setter for the end of this feature relative to the start of the slice that it is on. Note that negative values, or values exceeding the length of the slice are permitted. End must be greater than or equal to start regardless of the strand. Coordinate values start at 1 and are inclusive.

### Method
GET

### Endpoint
/feature/end

#### Query Parameters
- **end** (int) - Optional - The end position to set for the feature.

### Response
#### Success Response (200)
- **end** (int) - The end position of the feature.

#### Response Example
```json
{
  "end": 1500
}
```
```

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

### Setup Runnable for ExonerateCloneEnds in Perl

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1RunnableDB_1_1ExonerateClones

This snippet demonstrates the setup of a runnable object for ExonerateCloneEnds. It initializes parameters, including options if not provided, and then creates a new Bio::EnsEMBL::Analysis::Runnable::ExonerateCloneEnds instance with various configuration details.

```Perl
my %parameters = %{ $self->parameters_hash };

if (not exists( $parameters{-options} )
    and defined $self->OPTIONS) {
  $parameters{-options} = $self->OPTIONS;
}

#print STDERR "PROGRAM FILE: " . $self->analysis->program_file . "\n";

my $runnable = Bio::EnsEMBL::Analysis::Runnable::ExonerateCloneEnds->new(
  -program            => $self->analysis->program_file,
  -analysis           => $self->analysis,
  -target_file        => $target,
  -query_type         => 'dna',
  -query_file         => $query,
  -query_chunk_number => $chunk_number,
  -query_chunk_total  => $chunk_total,
  %parameters,
);

$self->runnable($runnable);
```

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

### Fetch Input Data and Setup Database Connections

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/HiveTranscriptCoalescer_8pm_source

The fetch_input method sets up the necessary environment for the HiveTranscriptCoalescer, including initializing the FASTA database, creating an analysis object, and establishing a database connection for the target database using DNA information.

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

  $self->setup_fasta_db;
  $self->create_analysis;
  my $dna_db = $self->get_database_by_name('dna_db');
  $self->hrdb_set_con($self->hrdb_get_dba($self->param_required('target_db'), $dna_db), 'target_db');
}
```

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

### Get Sequence Region Start (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1CircularSlice

Returns the start position of the slice relative to its sequence region. This method is an alias for the 'start()' method and is always in genomic coordinates.

```Perl
sub seq_region_start {
    my $self = shift;
    return $self->start();
}

```

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

### GET /get_genebuild_start_date

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/functions_func_0x67

Retrieves the start date of the genebuild.

```APIDOC
## GET /get_genebuild_start_date

### Description
Retrieves the start date for the genebuild process.

### Method
GET

### Endpoint
/get_genebuild_start_date

### Response
#### Success Response (200)
- **Data** (Bio::EnsEMBL::DBSQL::GenomeContainer) - The genebuild start date.

#### Response Example
```json
{
  "data": "Bio::EnsEMBL::DBSQL::GenomeContainer"
}
```
```

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

### Configure AnalysisSetup for Pipeline Initialization

Source: https://useast.ensembl.org/info/docs/Doxygen/production-api/classBio_1_1EnsEMBL_1_1Production_1_1Pipeline_1_1PipeConfig_1_1GeneNameDescProjection__plants__conf

Sets up the 'AnalysisSetup' module, responsible for initializing pipeline parameters and settings. It includes parameters like logic name, production lookup flag, delete existing flag, and the database backup file path. This analysis is configured with a specific resource class ('2GB').

```perl
-logic_name        => 'AnalysisSetup',
      -module            => 'Bio::EnsEMBL::Production::Pipeline::Common::AnalysisSetup',
      -analysis_capacity => 5,
      -max_retry_count   => 0,
      -parameters        => {
                              logic_name => $self->o('logic_name'),
                              production_lookup  => 1,
                              delete_existing => 1,
                              db_backup_file => catdir('#pipeline_dir#', '#config_type#', '#dbname#_bkp.sql.gz'),
                            },
      -rc_name           => '2GB',
    }
```

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

### Get Start Position of Slice (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1CircularSlice

Returns the start position of the slice. Coordinates are inclusive and start at 1. Negative coordinates or coordinates exceeding the sequence region length are permitted. Start is always less than or equal to end.

```Perl
sub start {
  my $self = shift;
  return $self->{'start'};
}

```

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

### Configuration and Parameter Methods

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/classBio_1_1EnsEMBL_1_1Analysis_1_1Hive_1_1RunnableDB_1_1HiveSelenocysteineFinder

Methods for managing configuration files, parameters, and module requirements.

```APIDOC
## ignore_config_file

### Description
Specifies that a configuration file should be ignored.

### Method
Not specified

### Endpoint
N/A

### Parameters
None

### Request Example
N/A

### Response
#### Success Response (200)
- **String** - A confirmation message or status.

#### Response Example
```
"Configuration file ignored."
```
```

```APIDOC
## input_id

### Description
Retrieves the current input identifier.

### Method
Not specified

### Endpoint
N/A

### Parameters
None

### Request Example
N/A

### Response
#### Success Response (200)
- **String** - The current input identifier.

#### Response Example
```
"input_12345"
```
```

```APIDOC
## input_id_array

### Description
Retrieves the current input identifiers as an array.

### Method
Not specified

### Endpoint
N/A

### Parameters
None

### Request Example
N/A

### Response
#### Success Response (200)
- **Arrayref** - An array of input identifiers.

#### Response Example
```json
["input_12345", "input_67890"]
```
```

```APIDOC
## input_is_void

### Description
Checks if the current input is empty or void.

### Method
Not specified

### Endpoint
N/A

### Parameters
None

### Request Example
N/A

### Response
#### Success Response (200)
- **String** - Returns '1' if input is void, '0' otherwise.

#### Response Example
```
"1"
```
```

```APIDOC
## no_config_exception

### Description
Handles exceptions related to missing configuration files.

### Method
Not specified

### Endpoint
N/A

### Parameters
None

### Request Example
N/A

### Response
#### Success Response (200)
None (throws an exception)

#### Response Example
N/A
```

```APIDOC
## param_defaults

### Description
Retrieves the default values for parameters.

### Method
Not specified

### Endpoint
N/A

### Parameters
None

### Request Example
N/A

### Response
#### Success Response (200)
- **Arrayref** - An array of default parameter values.

#### Response Example
```json
["default_value_1", "default_value_2"]
```
```

```APIDOC
## parameters_hash

### Description
Retrieves a hash of current parameters.

### Method
Not specified

### Endpoint
N/A

### Parameters
None

### Request Example
N/A

### Response
#### Success Response (200)
- **Hashref** - A hash containing the current parameters.

#### Response Example
```json
{
  "param1": "value1",
  "param2": "value2"
}
```
```

```APIDOC
## require_module

### Description
Ensures a specific Perl module is loaded and available.

### Method
Not specified

### Endpoint
N/A

### Parameters
* **module_name** (String) - Required - The name of the module to require.

### Request Example
N/A

### Response
#### Success Response (200)
None (loads the module if not already loaded)

#### Response Example
N/A
```

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

### Instantiate and Run HiveBlastRNASeqPep

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/HiveBlastRNASeqPep_8pm_source

Demonstrates how to create an instance of Bio::EnsEMBL::Analysis::RunnableDB::BlastRNASeqPep, fetch input data, run the analysis, and obtain the output. It requires a DBAdaptor object and an analysis object for configuration.

```perl
my $db    = Bio::EnsEMBL::DBAdaptor->new($locator);
my $btpep = Bio::EnsEMBL::Analysis::RunnableDB::BlastRNASeqPep->new (
              -dbobj      => $db,
              -input_id   => $input_id
              -analysis   => $analysis );

$btpep->fetch_input();
$btpep->run();
$btpep->output();
```

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

### Example TBlat Master Configuration (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/compara-api/AlignedMemberAdaptor_8pm

Example configuration files for using T-Coffee (TBlat) with a master-slave setup in Ensembl Compara. These Perl scripts demonstrate the setup for T-Coffee, a versatile multiple sequence alignment tool, in a distributed environment.

```perl
# Example: Bio/EnsEMBL/Compara/PipeConfig/Legacy/Example/TBlatMaster_conf.pm
package Bio::EnsEMBL::Compara::PipeConfig::Legacy::Example::TBlatMaster_conf;

use strict;
use warnings;

use Bio::EnsEMBL::Compara::PipeConfig::Basic_conf;

sub pipeline_ப்புகள் {
    my ($self) = @_;
    return (
        'TBlatMaster'
    );
}

1;

```

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

### Get Start Position

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/MappedSlice_8pm_source

Retrieves the start position of the container slice associated with this MappedSlice. This method navigates through the container and its contained slice to return the start coordinate. It requires no arguments.

```perl
sub start {
  my $self = shift;
  return $self->container->container_slice->start;
}
```

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

### Infernal RunnableDB: Initialize and Run

Source: https://useast.ensembl.org/info/docs/Doxygen/analysis-api/B_2Infernal_8pm_source

Demonstrates the initialization and execution of the Bio::EnsEMBL::Analysis::RunnableDB::Infernal module. This involves setting up the database connection, input ID, and analysis parameters, then fetching input, running the analysis, and writing the output.

```perl
my $runnableDB = Bio::EnsEMBL::Analysis::RunnableDB::Infernal->new(
            -db       => $db_adaptor,
    -input_id => $flag_id,
    -analysis => $analysis,
            );
$runnabledb->fetch_input();
$runnabledb->run();
$runnabledb->write_output();
```

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

### Get the start coordinate of the interval (Perl)

Source: https://useast.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Utils_1_1Interval

Returns the start coordinate of the interval region. Dependencies: None.

```Perl
sub start {
  my $self = shift;

  return $self->{start};
}

```
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