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: 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
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.
Looks as if there have been major changes to fasta36, see here:
Note in particular point 2:
I suggest submitting this as a bug report to GitHub along with the examples (use a gist, not pastebin as the latter are not around forever). We could add support for this (it’s not very high on our priority list of fixes), but having example files helps tremendously along that path. We also will acept any help/patches that get this working again :)
On Aug 7, 2014, at 7:47 PM, Antony03 <[hidden email]> wrote:
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Thank you for the answer. Do you if I can get more significant results with fasta35?
Depends on what you mean by ‘significant’; this is a question that probably belongs on a forum like Biostar or seqanswers.
The main thing is that the output is different enough that the latest releases will require additional work to get parsing working, but in the end may likely be more informative. On the other hand if you have highly repetitive data then it could generate a lot of noise. fasta35 may be completely sufficient depending what you are trying to do (which isn’t obvious here).
On Aug 7, 2014, at 9:29 PM, Antony03 <[hidden email]> wrote:
> Thank you for the answer. Do you if I can get more significant results with
> View this message in context: http://bioperl.996286.n3.nabble.com/fasta36-bug-report-tp17620p17622.html
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