[Bioperl-l] Status of assembly modules

Lee Katz lskatz at gatech.edu
Wed Nov 17 22:20:03 EST 2010

I have read on the BioPerl site that a 454 ace is not standardized due to
its coordinate system.  How can I convert it to the standard ace file?

When I run this code either by using contig or assembly objects, I get an
Can't call method "get_consensus_sequence" on an undefined value at
Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.

    sub _newblerAceToAce($args){
      #while(my $contig=$ace454->next_contig){
      while(my $scaffold=$ace454->next_assembly){
        print Dumper $scaffold;
      return $$args{acePath};

On Fri, Jun 18, 2010 at 5:59 AM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 13
> Date: Fri, 18 Jun 2010 15:39:39 +1000
> From: Florent Angly <florent.angly at gmail.com>
> Subject: [Bioperl-l] Status of assembly modules
> To: Joshua Udall <jaudall at gmail.com>,   bioperl-l List
>        <bioperl-l at lists.open-bio.org>
> Message-ID: <4C1B069B.5020105 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Hi Joshua,
> Yes, there have been interesting improvements in the assembly BioPerl
> module since v1.6.1. You can find these changes in the development
> version of BioPerl at http://github.com/bioperl/. I'll take this
> opportunity to introduce people who don't follow the commit messages to
> the new features that have been introduced:
> First, there is support for more file formats from high-throughput
> platforms, including those generated by de novo assembly and comparative
> assembly tools, such as:
>     * Roche 454 GS Assembler, aka Newbler (the ACE-454 variant)
>     * Maq
>     * Sam
>     * Bowtie
> There is support for running a lot more of these tools in Bioperl-run
> Bio::Tools::Run :
>     * Roche 454 GS Assembler, aka Newbler
>     * Minimo
>     * Maq
>     * Samtools
>     * Bowtie
> In terms of writing assembly file, I added the option to write ACE
> files, which is quite useful because maybe assembly programs recognize
> this format. So now you can read assemblies, modify them as you see fit
> and exporting them to other programs by writing the modified assembly in
> an ACE file.
> The internals of the IO parsers have acquired some granularity as it is
> now possible to read/write assembly files entirely, or one contig at a
> time. This is terrific to reduce memory usage.
> That's about it...
> Regards,
> Florent
> PS/ Josh, you filed bug reports related to several of these issues
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2726,
> http://bugzilla.open-bio.org/show_bug.cgi?id=2483). I am closing the
> ones that were not closed yet and thank you for submitting patches.
> On 18/06/10 14:00, Joshua Udall wrote:
> > Florent -
> >
> > I didn't want to ask a direct question on-list to perhaps avoid
> > confusion.  Were you able to improve/submit a ContigIO to bioperl that
> > works with one entry at a time (instead of slurping the entire ace
> > file)?
> >
> >

Lee Katz

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