Accession number same as contig name.

[nbisweden]

Accession number same as contig name.

[Juke34]

What I understand your purpose is not the submission to the ENA database but the creation of an EMBL file for a tool called IMG.

Instead of having

ID XXX; XXX; linear; genomic DNA; XXX; INV; 1351857 BP.
XX
AC XXX;
XX
AC * chr_1

you would like an option to get:

ID chr_1; XXX; linear; genomic DNA; XXX; INV; 1351857 BP.
XX
AC chr_1;
XX
AC * chr_1`

[caonetto]

Thanks for your reply. I had to replace the XXX values from the accession line that are meant to be filled up by ENA as this is incompatible with the JGI (Joint genome institute) upload pipeline. It might be a good idea to include this in the option parameters?

Thanks.

[Juke34]

I have modified the -a --accession option. It made no sense to be able to provide a value, because each record in the EMBL file would have a different accession number. So I have modified it to be a bolean. If you activate it, for each record the sequence name from the fasta file would become the accession.

Then, if the extra line AC * _chr1 needed for submission is problematic for your purpose, removing it using a sed command must be fine.