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#!/usr/bin/env perl

=pod

=head1 NAME

wgs2ncbi - prepares whole genome sequencing projects for submission to NCBI

=head1 SYNOPSIS

 Usage: wgs2ncbi [action] -conf [config file]

Typically, you will run the following sequence of commands:

 $ wgs2ncbi prepare -conf config.ini
 $ wgs2ncbi process -conf config.ini
 $ wgs2ncbi convert -conf config.ini
 $ wgs2ncbi prune -conf config.ini
 $ wgs2ncbi trim -conf config.ini
 $ wgs2ncbi compress -conf config.ini

The C<prepare> and C<compress> steps will be one time operations, but C<process>,
C<convert>, C<trim> and C<prune> may be iterative, depending on the feedback you will get 
from NCBI (e.g. about invalid product names, unmasked adaptor sequences, and other 
problematic regions).

=head1 DESCRIPTION

C<wgs2ncbi> is a script that helps users prepare submissions of annotated, whole genomes 
to NCBI. It does this by performing a number of actions that need to be taken in sequence. 
Each of these actions need to be invoked as a subcommand (i.e. C<wgs2ncbi [action]>), 
which will run for a certain amount of time. The actions are documented more fully in the 
module of functions that this script is based on. Links to the respective, expanded 
documentation sections are given below. Here follows a brief description of the actions:

=head2 C<prepare>

Prepares the rest of the procedure by expanding the single genome annotation file into 
separate files, one for each contig. See L<Bio::WGS2NCBI/prepare>.

=head2 C<process>

Processes the genome by writing out feature tables and masking contig segments as needed.

=head2 C<convert>

Converts the masked contigs and feature tables into ASN.1 using tbl2asn.

=head2 C<prune>

Based on a validation file from NCBI, makes pruned versions of feature tables that omit
features within regions identified by NCBI.

=head2 C<trim>

Trims leading and trailing NNNs from sequence files and feature tables.

=head2 C<compress>

Packs the ASN.1 files into a .tar.gz archive for upload to NCBI.

=cut

# in case people don't want to install, they can just add this script 
# to their PATH and the rest should be picked up automatically.
BEGIN {
	use FindBin '$Bin';
	use lib "$Bin/../lib";
}

use Bio::WGS2NCBI;

# shift the subcommand from @ARGV so that the remainder can be parsed
# by the config object using Getopt::Long.
my $action = shift;

# despatch to the subcommand
if ( $action and Bio::WGS2NCBI->can($action) ) {
    Bio::WGS2NCBI->$action;
    exit 0;
}

# if no subcommand was given, display help docs and quit
Bio::WGS2NCBI->help;