genomer-validate(1) -- Test assembly files for errors
=====================================================

## SYNOPSIS

`genomer validate` <type>

## DESCRIPTION

**Genomer-validate** tests the assembly files for errors. Any detected errors 
are reported to the terminal.

## OPTIONS

  * `--no_view_validations`
    The GFF ninth-column attributes are validated to ensure that all attributes 
    beginning with a lower case character match those used by 
    genomer-plugin-view to generate GenBank annotation table output. This 
    argument can be used to disable these validations.

## FILE TYPES

### ANNOTATIONS

Test the annotation file for errors. The default location for this file is 
**assembly/annotations.gff**. The following validations are performed:

  * `Identical locations`:
    Flag annotations of the same type with identical start and end coordinates.

  * `Identical IDs`:
    Flag two or more annotations identical ID attributes.

  * `Missing ID`:
    Flag annotations without an ID attribute.

  * `Missing either Name or product`:
    Flag annotations without either a Name or product attribute.

  * `Capitalised Name attribute`:
    Flag annotations with Name attributes beginning with an uppercase letter.

  * `Invalid GFF attributes`:
    Flag annotations with capitalised attribute keys outside of the GFF3 
    vocabulary. See below for a description of this vocabulary.

  * `Invalid genomer plugin view attributes`:
    Flag annotations with attribute keys outside of the genomer-plugin-view 
    vocabulary. This validation can be disabled using the `--validate_for_view` 
    command line flag.

  * `Bad product fields`: NCBI requires that annotation product fields not
  contain terms such as "putative" or end with "-like." This validator checks
  that product fields do not contain the more common types of disallowed terms. 

The [GFF3 specification][http://www.sequenceontology.org/gff3.shtml] restricts 
attributes beginning with an upper case character (A-Z) in the ninth column to 
a controlled vocabulary. Any attribute keys appearing in the ninth column not 
included in this vocabulary will raise a validation error. The allowed keys are 
listed below. The ID field is considered mandatory in this software and will 
raise an error if not present.

  * ID
  * Name
  * Note
  * Alias
  * Parent
  * Target
  * Gap
  * Derives\_from
  * Dbxref
  * Ontology\_term
  * Is\_circular

Any fields beginning with a lower case character (a-z) are allowed in the GFF3 
ninth column. The genomer-plugin-view however uses these lower case fields to 
populate a GenBank annotation table and a validation is performed for this.
The optional `--no_view_validations` flag can be used to disable this 
validation. The allowed genomer-plugin-view attribute keys are as follows:

  * product
  * ec\_number
  * function
  * feature\_type

## EXAMPLES

Test the annotation file for errors.

    $ genomer validate annotations

## BUGS

**Genomer-validate** is written in Ruby and depends on the genomer gem. See the 
Gemfile in the genomer-plugin-validate gem install directory for version 
details.

## COPYRIGHT

**Genomer** is Copyright (C) 2012 Michael Barton <http://michaelbarton.me.uk>