Closed ardy20 closed 3 years ago
I have faced the same issue by using maf alignment created with SibeliaZ.
Hi,
For the maf workflow, you need to have your fasta sequence names in a form genome.chromosome
, where genome
is the same name you are using in the recipe file, and chromosome
is any unique identifier.
Mikhail
Thanks Mikhaeil My fasta file has 250 contigs. Is there any tool or script that can do this? Regards Ardy
On Tue, 15 Dec 2020 at 3:41 am, Mikhail Kolmogorov notifications@github.com wrote:
Hi,
For the maf workflow, you need to have your fasta sequence names in a form genome.chromosome, where genome is the same name you are using in the recipe file, and chromosome is any unique identifier.
Mikhail
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Regards
Ardy Kharabian-Masouleh (PhD)
Email: kharabian1@gmail.com
a.kharabianmasouleh@uq.edu.au
Mobile: +61405134478
I'm not aware of any scripts, unfortunately.
Dear Mikhaeil, You can do it by using awk with following command awk '/^>/{print ">genome.chromosome" ++i; next}{print}' < file.fasta > output.fasta
Hi
I am trying to run Ragout using a .maf alignment file created with SibeliaZ. But I get the following error:
ERROR: An error occured while running Ragout: ERROR: permutation ids in /ragout/results/maf-workdir/100/blocks_coords.txt do not follow naming convention: 'genome.chromosome'
Could you please explain which file should I change and how? Is there any script for that?
Regards Ardy