[Bioperl-l] Parsing FASTA m10 output

Chris Fields cjfields at uiuc.edu
Mon Apr 23 08:46:40 EDT 2007


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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