[Bioperl-l] How to print a generic matrix?

Jordan Mark Swanson swansonj at email.arizona.edu
Fri Mar 3 16:40:09 EST 2006


On Fri, 3 Mar 2006 13:18:20 -0800 (PST), "Sam Al-Droubi"
<saldroubi at yahoo.com> said:
> Jordan,
>   
>   Thank you for your responss.  I relatively new to informatics and  I
>   don't know what the different matrix formats are.  Where is this 
>   documented.  Would be a good idea for me to complete these  functions
>   and submit them to be inculded in MatrixIO?

I haven't used the modules we are discussing, but to find information
about them I changed to the directory Bio/Matrix/IO and noted which
files were in there.  It appears that there is a scoring matrix and a
phylip matrix.  The phylip matrix seems to have an output method
written, but I don't know if it would be appropriate for your needs. 
Perhaps someone else could help you more.


To find different module formats for Bio::Matrix::IO  :
[jswanson at localhost bioperl-live]$ cd Bio/Matrix/IO
[jswanson at localhost IO]$ ls
CVS/  phylip.pm  scoring.pm

This is analagous to what you would do to find SeqIO modules :
...
[jswanson at localhost bioperl-live]$ cd Bio/SeqIO
[jswanson at localhost SeqIO]$ ls
abi.pm        bsml.pm      ctf.pm         fasta.pm     gcg.pm        
locuslink.pm  pln.pm    tab.pm      ztr.pm
ace.pm        bsml_sax.pm  CVS/           fastq.pm     genbank.pm    
metafasta.pm  qual.pm   tigr.pm
agave.pm      chadoxml.pm  embl.pm        FTHelper.pm  interpro.pm   
MultiFile.pm  raw.pm    tigrxml.pm
alf.pm        chaos.pm     entrezgene.pm  game/        kegg.pm       
phd.pm        scf.pm    tinyseq/
asciitree.pm  chaosxml.pm  exp.pm         game.pm      largefasta.pm 
pir.pm        swiss.pm  tinyseq.pm

-- 
  Jordan Swanson
  swansonj at email.arizona.edu
  Genetics Graduate Interdisciplinary Program
  University of Arizona



More information about the Bioperl-l mailing list