[Bioperl-l] fasta36 bug report

[Antony03]

Hello,

There is a problem when I try to parse a fasta36 report. I got this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unrecognized alignment line (3) '>--'
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::SearchIO::fasta::next_result
/usr/share/perl5/Bio/SearchIO/fasta.pm:1148
STACK: ./Auto_Annot.pl:123
-----------------------------------------------------------

There is a '>--' after each alignment in fasta36 but not in fasta35. 

Consequently, I tried to parse a fasta35 alignment. There is no problem with
bioperl. However, the result is clearly not the same between both (fasta35
and fasta36).

fasta35 gives only 1 alignment: http://pastebin.com/f4NdYJCt

while fasta36 gives 3 alignments: http://pastebin.com/ADeKJ4GC

What I'm doing wrong with fasta35? It is probably not normal that it misses
almost 2 perfect alignments on 3.

Thanks you!




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