[Biopython-dev] unsubscribe

Thomas van Gurp thomasvangurp at gmail.com
Sun Aug 8 09:55:11 UTC 2010 

2010/8/5 <biopython-dev-request at lists.open-bio.org>

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> Today's Topics:
>
>   1. Re: Newbler ACE file to SAM?
>      (Kevin Jacobs <jacobs at bioinformed.com>)
>   2. [Bug 3130] New: Broken links in Documentation to  NCBI Blast
>      (bugzilla-daemon at portal.open-bio.org)
>   3. Re: Newbler ACE file to SAM?
>      (Kevin Jacobs <jacobs at bioinformed.com>)
>   4. Re: Newbler ACE file to SAM?
>      (Kevin Jacobs <jacobs at bioinformed.com>)
>   5. [Bug 3130] Broken links in Documentation to NCBI  Blast
>      (bugzilla-daemon at portal.open-bio.org)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 4 Aug 2010 13:32:22 -0400
> From: "Kevin Jacobs <jacobs at bioinformed.com>" <bioinformed at gmail.com>
> Subject: Re: [Biopython-dev] Newbler ACE file to SAM?
> To: Peter <biopython at maubp.freeserve.co.uk>
> Cc: "biopython-dev at biopython.org" <biopython-dev at biopython.org>
> Message-ID:
>        <AANLkTim0+8t5wb5wbNw1varNPxNuRi4WdZKPD1D6+NXO at mail.gmail.com<AANLkTim0%2B8t5wb5wbNw1varNPxNuRi4WdZKPD1D6%2BNXO at mail.gmail.com>
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Aug 4, 2010 at 1:24 PM, Peter <biopython at maubp.freeserve.co.uk
> >wrote:
>
> > On Wed, Aug 4, 2010 at 6:12 PM, Kevin Jacobs wrote:
> > > On Wed, Aug 4, 2010 at 1:10 PM, Peter wrote:
> > >>
> > >> Or ask your Roche representatives to implement SAM/BAM output?
> > >> Mind you, as the MIRA3 author has pointed out, SAM/BAM isn't so
> > >> great for de novo assemblies. It doesn't even store the contig seq ;)
> > >>
> > >
> > > They're working on it.  :)
> > > -Kevin
> > >
> >
> > Do you mean Roche are working on SAM/BAM output? If so, that's good news.
>
>
>
> Yes, I believe that Roche is working on SAM/BAM support for a future
> version
> of Newbler.  As of a few weeks ago, when I last spoke to them, they were
> just gathering information and had yet to start on the implementation.  I'd
> expect to see this feature with Newbler 2.6 (supporting the same features
> as
> 2.5 on the FLX, which was for the Jr only) or more likely with the
> subsequent  2.7 release.  In other words, I'd be surprised to see it in the
> coming weeks or few months.
>
>
> > If you mean the SAM/BAM format, I'm on the samtools-devel list where
> > they are discussing several specification improvements/additions, but
> > I don't recall anything specifically aimed at de novo assemblies.
> >
> >
> I didn't see the Roche folks in that discussion, but I'll look again.  As
> far as I know, they're not looking to change or alter the spec, but I could
> easily be wrong.  I do keep in contact with a few of the folks at Roche,
> but
> have no deep insight into their future plans.
>
> -Kevin
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 4 Aug 2010 14:00:37 -0400
> From: bugzilla-daemon at portal.open-bio.org
> Subject: [Biopython-dev] [Bug 3130] New: Broken links in Documentation
>        to      NCBI Blast
> To: biopython-dev at biopython.org
> Message-ID: <bug-3130-42 at http.bugzilla.open-bio.org/>
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=3130
>
>           Summary: Broken links in Documentation to NCBI Blast
>           Product: Biopython
>           Version: Not Applicable
>          Platform: All
>               URL:
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.htm
>                    l
>        OS/Version: All
>            Status: NEW
>          Severity: normal
>          Priority: P2
>         Component: Documentation
>        AssignedTo: biopython-dev at biopython.org
>        ReportedBy: mphillip at vt.edu
>
>
> The links to NCBI Blast in 7.1 of the Biopython Tutorial and Cookbook,
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html, are broken
> (they
> lead to HTTP 404 pages):
>
> http://www.ncbi.nlm.nih.gov/BLAST/blast_program.html should possibly be
> http://www.ncbi.nlm.nih.gov/BLAST/blast_program.shtml
>
> http://www.ncbi.nlm.nih.gov/BLAST/blast_databases.html should possibly be
> http://www.ncbi.nlm.nih.gov/BLAST/blast_databases.shtml
>
>
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>
> ------------------------------
>
> Message: 3
> Date: Wed, 4 Aug 2010 16:41:06 -0400
> From: "Kevin Jacobs <jacobs at bioinformed.com>" <bioinformed at gmail.com>
> Subject: Re: [Biopython-dev] Newbler ACE file to SAM?
> To: Nick Loman <n.j.loman at bham.ac.uk>
> Cc: "biopython-dev at biopython.org" <biopython-dev at biopython.org>
> Message-ID:
>        <AANLkTinTeRP44x3AoY+PCfYi7v1gHgc6SgmBZP9Yz9cC at mail.gmail.com<AANLkTinTeRP44x3AoY%2BPCfYi7v1gHgc6SgmBZP9Yz9cC at mail.gmail.com>
> >
> Content-Type: text/plain; charset=windows-1252
>
> On Wed, Aug 4, 2010 at 12:32 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
>
> > I'm pretty sure the ACE files contain the individual reads (or at the
> > least, the trimmed, aligned portions of them) because this is the file
> one
> > uses in Consed/Tablet to view an assembly. We may of course be talking at
> > cross-purposes!
> >
> >
> Hi Nick,
>
> I've reviewed the Newbler ACE files and re-discovered the reason why they
> weren't ideal in the first place: the alignment records in Newbler?s output
> are gapped based on a pseudo-multiple-alignment of all of the reads to the
> reference, not a standard pairwise alignment.  So there is no easy way to
> differentiate which gaps in each read were introduced as part of the
> pairwise alignment or as artifacts of the multi-way alignment.  This means
> I'd need to  re-compute the alignment to the reference, but should be
> relatively easy since the aligned start position is known using a round of
> the standard Smith-Waterman algorithm.
>
> In other words, it is technically possible to use Newbler's ACE files, but
> it really is simpler and easier to use the 454PairAlign.txt results.  More
> so because the 454PairAlign.txt files are often vastly smaller than
> 454Contig.ace files.
>
> On the other hand, it should be easy to adapt my scripts to convert
> non-Newbler ACE files to SAM/BAM provided that the reads are gapped for
> pairwise alignment.  It has been so long since I've used consed/phred/phrap
> that I don't remember if this is how it is normally done.
>
> -Kevin
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 4 Aug 2010 16:44:25 -0400
> From: "Kevin Jacobs <jacobs at bioinformed.com>" <bioinformed at gmail.com>
> Subject: Re: [Biopython-dev] Newbler ACE file to SAM?
> To: Nick Loman <n.j.loman at bham.ac.uk>
> Cc: "biopython-dev at biopython.org" <biopython-dev at biopython.org>
> Message-ID:
>        <AANLkTin_41diNtE3LVOfw=3yz8sYS5mJU5TpuergvQts at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Aug 4, 2010 at 4:41 PM, Kevin Jacobs <jacobs at bioinformed.com> <
> bioinformed at gmail.com> wrote:
>
> > On Wed, Aug 4, 2010 at 12:32 PM, Nick Loman <n.j.loman at bham.ac.uk>
> wrote:
> >
> >> I'm pretty sure the ACE files contain the individual reads (or at the
> >> least, the trimmed, aligned portions of them) because this is the file
> one
> >> uses in Consed/Tablet to view an assembly. We may of course be talking
> at
> >> cross-purposes!
> >>
> >>
> > I've reviewed the Newbler ACE files and re-discovered the reason why they
> > weren't ideal in the first place:
> >
>
> Never mind-- I didn't realized the consensus sequence was gapped, so it is
> then trivial to recover the original pairwise alignments.  I'll have a
> version of my Newbler2SAM module that can process ACE files shortly.
>
> -Kevin
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 4 Aug 2010 17:14:30 -0400
> From: bugzilla-daemon at portal.open-bio.org
> Subject: [Biopython-dev] [Bug 3130] Broken links in Documentation to
>        NCBI    Blast
> To: biopython-dev at biopython.org
> Message-ID: <201008042114.o74LEUCs030000 at portal.open-bio.org>
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=3130
>
>
>
>
>
> ------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2010-08-04 17:14 EST -------
> Confirmed.
>
> I wonder why the NCBI changed this without putting redirects in place?
>
>
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> End of Biopython-dev Digest, Vol 91, Issue 7
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-- 
Met vriendelijke Groet,
Thomas van Gurp

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