On Thu, Nov 10, 2011 at 8:33 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi Martin,
>
> On Thu, Nov 10, 2011 at 10:37 PM, Martin Morgan <mtmorgan@fhcrc.org>
> wrote:
> > On 11/09/2011 03:22 AM, Yating Cheng wrote:
> >>
> >> Dear Bioconductor Memebers,
> >>
> >> Now I have to extract intron sequences, I have already exon+intron,
> intron
> >> sequences. Someone told me that I can use Biostring. But I tried, it
> >> failed.
> >>
> >> Do you know how to use Biostring to solve this problem, or is there any
> >> other possibility to solve this problem?
> >
> > Steve and Ivan mention GRanges + BSgenome. I wanted to mention
> > Rsamtools::FaFile with indexFa, which allows input of DNA sequence from
> > fasta files rather than BSgenome packages. You gain flexibility in terms
> of
> > where the sequence comes from, but lose BSgenome features like masking
> and
> > data management.
>
> That's super cool! Thanks for adding that
>
> This means that we have to keep those *.fa files uncompressed tho,
> right? I wonder if it's worth thinking about (for R 2.15 ;-) handling
> compressed *.fa files using BGZF along these lines, too:
>
> http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html
>
>
Actually, the FaFile stuff uses RAZF compression, another extension of gzip.

Just to add another plug, the rtracklayer package now supports sequence
from 2bit files. This was mostly motivated by the fact that the RAZF
compression is not well supported in Java, so Java tools typically support
2bit. It also supports a single mask, although importing of the mask is not
yet supported in rtracklayer. Not sure about how the two formats compare in
terms of compactness, but 2bit is obviously highly compact (2 bits per
base). While size does not matter so much these days, it may make a
difference in query speed. There, 2bit has the advantage of random access,
whereas the RAZF stuff sounds more complex.


-steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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