[Bioperl-l] Parsing FASTA m10 output

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Mon Apr 23 09:29:39 EDT 2007


Since -m10 is newer than PGM_DOC, you should be fine to use the first line 
as a detection for m10, when that first line exists (when it does not, the 
format cannot be m10, unless someone has re-compiled FASTA with an 
undefined PGM_DOC).

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 04/23/2007 08:46:40 AM:

> That's true, but older versions of fasta don't do this.  For 
> instance, the example files in the bioperl distribution in t/data 
> (HUMBETGLOA.FASTA, cysprot1.fasta, cysprot_vs_gadfly.fasta) lack this 
> line.
> 
>  From the fasta changelog:
> 
> -------------------------------------------------------------
>  >>Nov 14-22, 2002  CVS fa34t20b6
> 
> Include compile-time define (-DPGM_DOC) that causes all the fasta
> programs to provide the same command line echo that is provided by the
> PVM and MPI parallel programs.  Thus, if you run the program:
> 
>      fasta34_t -q -S gtt1_drome.aa /slib/swissprot 12
> 
> the first lines of output from FASTA will be:
> 
>      # fasta34_t -q gtt1_drome.aa /slib/swissprot
>       FASTA searches a protein or DNA sequence data bank
>       version 3.4t20 Nov 10, 2002
>      Please cite:
>       W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
> 
> This has been turned on by default in most FASTA Makefiles.
> -------------------------------------------------------------
> 
> We could only support newer fasta output (newer that the above 
> version) since there have been several bug fixes and changes to 
> output; not sure how everyone else feels about this.
> 
> chris
> 
> On Apr 23, 2007, at 4:45 AM, Ioannis Kirmitzoglou wrote:
> 
> > I don't know about older versions but the latest version of FASTA 
> > starts its
> > output with a line similar to those:
> > # fasta34.exe -m9 -d0 -Q test.faa test.faa OR
> > # fasta34.exe -m10 -Q test.faa test.faa
> >
> > This very first line is also the only one in the output that starts 
> > with
> > '#'.
> > Isn't this an easy way to determine the output type?
> >
> >
> > -- 
> >
> > *Ioannis Kirmitzoglou*, MSc
> > PhD. Student,
> > Bioinformatics Research Laboratory
> > Department of Biological Sciences
> > University of Cyprus
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
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