Bio-WGS2NCBI

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README.md  view on Meta::CPAN

- [Before you start](#before-you-start) - set up all the input files, prepare a submission
  template
- [Subcommand `prepare`](#subcommand-prepare) - pre-process the annotation file for rapid
  access in the following steps
- [Subcommand `process`](#subcommand-process) - convert the genome file and annotations
  to FASTA chunks and feature tables
- [Subcommand `convert`](#subcommand-convert) - runs tbl2asn to convert the FASTA chunks
  and feature tables to SeqIn files
- [Subcommand `compress`](#subcommand-compress) - collates the SeqIn files into a single
  archive for upload to NCBI      

Before you start
----------------

Before issuing any commands, the following steps need to be taken:

1. The installation (see above) needs to be completed.
2. You need to have the genome assembly available as a FASTA file, and the annotations
   as a GFF3 file.
3. You will need to prepare a 

README.md  view on Meta::CPAN

> command-line program asndisc.
>
> If you have questions about the Discrepancy Report, please contact us by email at 
> genomes@ncbi.nlm.nih.gov prior to sending us your submission.
Source: https://www.ncbi.nlm.nih.gov/genbank/asndisc/

Subcommand `compress`
---------------------

The final step simply takes the `.sqn` files from the previous step and combines them in
a single `.tar.gz` archive for upload to the NCBI submission portal. No data processing of
any kind takes place, this is purely for convenience and is executed as follows:

    $ wgs2ncbi compress -conf <config.ini>
    
i.e. by providing the location of the [wgs2ncbi.ini](share/wgs2ncbi.ini) configuration 
file to the `-conf` argument. The following will then happen:

- all .sqn files are combined in a single archive, whose location is specified by
  [archive](https://github.com/naturalis/wgs2ncbi/blob/master/share/wgs2ncbi.ini#L42)

You will then upload the produced archive to the submission portal. Once you upload the 
archive, you will get a verdict from whoever is handling this submission at NCBI. 
Depending on their feedback, you will likely have to update the configuration files a few
more times to correct for spurious sequence data and gene product names, after which you
will re-run the `process` subcommand (and onwards to `convert` and `compress`).

About this software
===================

WGS2NCBI is implemented as a Perl5 package. It is open source software made available
under the [BSD3 license](LICENSE).

lib/Bio/WGS2NCBI.pm  view on Meta::CPAN

				# still here? then print the feature
				print $fh $feat->to_string;
			}
		}	
	}	
}

=head1 compress

The C<compress> action bundles the ASN.1 files produced by C<Bio::WGS2NCBI/convert> into
a .tar.gz archive that can be uploaded to NCBI. This requires the following configuration 
settings:

=over

=item C<outdir>

The location where the ASN.1 files were written.

=item C<archive>

script/wgs2ncbi  view on Meta::CPAN

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";
}