Re: [MUMmer-help] Mapview help

[Adam P. <ada...@ya...>]

Hello Apoorv,
Your GFF file is probably fine and you are running the program correctly,  but there is a bug in mapview that forces it to only accept annotations of the form initial-exon, single-exon, last-exon. So, since you are running this on a prokaryotic genome with no introns, your GFF file probably has annotations of the form "gene". If you replace all the "gene" occurrences in your file with "single-gene" it should work. This really is a nuisance, so I'll fix the code for the next release. The original author of mapview is no longer affiliated with the project, but I've looked at the code before and it should be an easy fix.

Best,
Adam Phillippy

"Kalra, Apoorv" <ak...@me...> wrote: I'm trying to get the annotations onto the mapview figure.

I can successfully create the mapview figure without the annotations. The
documentation suggests I just need to supply a cds or utr file's in gff format
after the mapview command.
The following command works fine, producing a figure called abyshori.gif:
mapview -n 1 -p abyshori abyshori.coords


I have been to ncbi and retrieved the gff file for pyrococcus abyssi
(ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Pyrococcus_abyssi/NC_000868.gff),
saving it into a file called abys.gff. However, when I execute the following
command:
mapview -n 1 -p abyshori abyshori.coords abys.gff
I recieve the following error:
 ERROR in the input files ! The reference seq ID can't be found in GFF files !
      The first column in the GFF file should be the ID of the reference seq.
      The alignments file should provide the same info in the column before the
last one.

It continues with an example of the proper format. The file NC_000868.gff
appears to be in the correct format as far as I can tell. I've made sure that
reference file sequence id is the same as the the id appearing in the first
column of the gff file (NC_000868.1), run that through promer and I get the
same error message. If I'm meant to be getting a different gff formatted file
off ncbi, I can't find it.

Can anyone offer me some pointers on this? I'm not sure what more I should be
looking for in the formatting of the files.

Thanks.





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