Contig separation from .ace files

[MikeT]

Greetings,
I'm working on an assembly of multiple metagenomic datasets using CAP3. I'd like to select and export from the assembly only contigs generated by reads coming from specific datasets and then annotate them separately. Is there a way (script, software or anything else) to do the extraction?
Best regards

-MikeT

[TiborNagy]

Hi,

In ACE format the contig start from the CO tag (line begins with it) until BQ tag.

[MikeT]

Hi,

In ACE format the contig start from the CO tag (line begins with it) until BQ tag.

Thank you, but I already know how to "read" an .ace file.
My problem is: I have lots of different contigs, created from the assembly of 10 different metagenomes. I just want to see only the contigs created by the assembly of multiple metagenomes and extract them. For example, I might need the contig created by reads coming from sample 1, 3, and 6, the contig created by reads coming from sample 4 and 5, and so on, and I need to have them on a separate file.
I just can't manually skim over an entire assembly, I don't have enough time, so how can I do it in another way?

-MikeT

[maubp]

I think what TiborNagy is implying is that the ACE file format is quite simple to break into contigs in a script, so you should be able to do this yourself in Python/Perl/Ruby/etc.

[TiborNagy]

Well, in this case I suggest BioPerl/BioPython. You can easily write scripts using those APIs.