[Bioperl-l] Split ACE file by AGP scaffolds

Florent Angly florent.angly at gmail.com
Wed Jan 11 17:40:12 EST 2012


Hi Nathan,

I am not familiar with AGP files, but I do not think that Bioperl can 
read them. However, to process the contigs in your ACE file, you can use 
Bio::Assembly::IO::ace : 
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Assembly/IO/ace.html 

The synopsis has snippets of code to get you started. Since you want to 
read and write contigs individually, you probably want to use these 
methods: next_contig, write_header, write_contig, write_footer

What do you plan on doing with Consed? There are alternatives you could 
try to vizualize your assembly, e.g. Hawkeye, from the AMOS package.

Best,

Florent


On 11/01/12 16:42, Nathan Watson-Haigh wrote:
> I have an ACE file (500k contigs>  500bp) generated by Newbler for a 450MB genome which I'd like to open in consed. However, due to its size and my computer memory limits it only opens 10-15%.
>
> I'm trying to spilt the ACE file into smaller subsets of contigs which i can handle in consed.
>
> I think a valid approach is to generate an ACE file per scaffold and work in consed on each scaffold in turn. Does this sound valid?
>
> If i take the AGP file that Newbler generated, i should be ankle to take the monolithic ACE file and split it into 20k ACE files representing each scaffold.
>
> Does anyone have thoughts on whether this is doable with the BioPerl with the Bio::Assembly:IO:ace module? If so, could you give me a couple of quick pointer?
>
> Cheers, Nath
>
> Sent from my Android phone.
>
>
> Nathan Watson-Haigh
> Senior Bioinformatician  | The Australian Wine Research Institute
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