[Bioperl-l] Problems of parse emboss water result by Bio::AlignIO

zeroliu zeroliu at 163.com
Mon Aug 27 07:49:53 EDT 2007


 Hello,
I'm trying to parse water (EMBOSS 5.0.0) result by Bio::AlignIO
(Bioperl-1.4) and encountered some problems.
1. What does the Bio::AlignIO->next_aln() return?
Does it return a Bio::Align::AlignI or Bio::SimpleAlign object?
Or it depends on the alignment file format?
2. How can I get the "score" properity in a water alignment result?
There is a score method in Bio::SimpleAlign but not in Bio::AlignIO.
In 2004, Jason mentioned:
Scores are set by the Alignment parser - we separate the 'running' from
the 'parsing'.
Bio::AlignIO::emboss had to be updated.
(http://article.gmane.org/gmane.comp.lang.perl.bio.general/7156/match=alignio+water)
How could I know it?
Thank you very much!  


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