[BioC] Biostring: print sequence alignment to file

[Thomas Girke]

What about providing an option in pairwiseAlignment to output to the 
MultipleAlignment class in Biostrings and then write the latter to 
different alignment formats? 

Thomas

On Tue, Apr 17, 2012 at 05:59:24PM +0000, Hervé Pagès wrote:
> Hi Martin,
> 
> On 04/16/2012 04:06 AM, Martin Preusse wrote:
> > Hi Charles,
> >
> > thanks! Your solution allows to print the two alignment strings separately.
> >
> > I was thinking of an output as generated by alignment tools:
> >
> > AGT-TCTAT
> > | | | |  |  | | | |
> > AGTATCTAT
> 
> This looks like BLAST output. Is this what you have in mind? Note that
> there are many alignment tools and many ways to output the result to a
> file. I'm not really familiar with the BLAST output format. Is it
> specified somewhere? Would that make sense to add something like a
> write.PairwiseAlignedXStringSet() function to Biostrings for writing
> the result of pairwiseAlignment() to a file? We could do this and
> support the BLAST format if that's a commonly used format.
> 
> Thanks,
> H.
> 
> >
> > For this I would have to write a function to output the strings in blocks of e.g. 60 nucleotides, right?
> >
> > Cheers
> > Martin
> >
> >
> >
> > Am Freitag, 13. April 2012 um 19:21 schrieb Chu, Charles:
> >
> >> write.XStringSet
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor