[genoPlotR-help] genePlotR 0.5.5 bug - can't load mauve alignment

[Lionel Guy]

Dear Christian,

Thanks for your interest in genoPlotR. 
I think the problem comes from the way you are reading the backbone file. The command system.file, that is used in the example, will give the path to a file that is distributed with the package, which is the case for the Bartonella 4 genomes example. In your case, you want to read directly your file, like this:

back <- read_mauve_backbone('/home/cklatt/Desktop/FAP_genomes/mauve_fap_align_gb.backbone')

HTH,

Lionel

On 1 Dec 2010, at 19:39 , Christian G. Klatt wrote:

> Dear Dr. Guy,
> 
> Thank you for your development of a very useful tool.
> 
> I am having difficulty loading a Mauve progressive alignment (produced using Mauve 2.3.1) of 8 bacterial genomes, two of which were originally input into mauve as genbank files, and two which were input as FASTA files (thus lacking any feature annotation).
> 
> I've attached the .backbone data file and the code I used below - I was curious if this was reproducible.
> 
> The example code for the four Bartonella genomes works fine.
> 
> I'm using R 2.11.1 and genePlotR 0.5.5 on Ubuntu Maverick 10.10.  The same problem occurred on genePlotR 0.5.4.
> 
> Apologies if I've missed something obvious!
> 
> Thank you for your time,
> -Chris
> 
> CODE and OUTPUT:
> 
> > library(genoPlotR)
> Loading required package: grid
> Loading required package: ade4
> 
> Attaching package: 'ade4'
> 
> The following object(s) are masked from 'package:base':
> 
>    within
> 
> > back_file <- system.file('/home/cklatt/Desktop/FAP_genomes/mauve_fap_align_gb.backbone', package='genoPlotR')
> > back <- read_mauve_backbone(back_file)
> Error in read.table(file, stringsAsFactors = FALSE, header = header) :
>  no lines available in input
> In addition: Warning message:
> In file(file, "rt") :
>  file("") only supports open = "w+" and open = "w+b": using the former
> >
> 
> -- 
> Christian Klatt
> Ph.D. Candidate
> Department of Land Resources
> and Environmental Sciences
> 334 Leon Johnson Hall
> P.O. Box 173120
> Montana State University - Bozeman
> Bozeman, MT 59717-3120
> 
> phone: 406-994-3412
> FAX: 406-994-3933
> 
> <mauve_fap_align_gb.backbone>

============================================
Lionel Guy
Molecular Evolution, EBC, Uppsala University
Norbyv. 18C, 752 36  Uppsala, Sweden

phone: +46 (0)18-471 6129
fax : +46 (0)18-471 6404
email: lionel.guy at ebc.uu.se
============================================