[Bioperl-l] Split ACE file by AGP scaffolds
florent.angly at gmail.com
Wed Jan 11 17:40:12 EST 2012
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
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.
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
> Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 | Map
> PO Box 197, Glen Osmond SA 5064, Australia
> T: +61 8 83136836 (direct) | F: +61 8 83136601 |
> www: www.awri.com.au | AWRI Events
> This communication, including attachments, is intended only for the addressee(s) and contains information which might be confidential and/or the copyright of The Australian Wine Research Institute (AWRI) or a third party. If you are not the intended recipient of this communication please immediately delete and destroy all copies and contact the sender. If you are the intended recipient of this communication you should not copy, disclose or distribute any of the information contained herein without the consent of the AWRI and the sender. Any views expressed in this communication are those of the individual sender except where the sender specifically states them to be the views of the AWRI. No representation is made that this communication, including attachments, is free of viruses. Virus scanning is recommended and is the responsibility of the recipient.
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l