[Bioperl-l] "Be forgiving in what you accept" andBio::Tools::GuessSeqFormat

George Hartzell hartzell at kestrel.alerce.com
Fri Jul 22 11:35:47 EDT 2005

Nathan Haigh writes:
 > May I ask what software is producing this FASTA format file which has a
 > space immediately after the '>' in the description line?

I don't know what created it.  Wouldn't surprise me to find out it was
created in Microsoft Word....  It was given to me as a example input
file/test case.

 > Although I am not aware of a formal description of FASTA format, I have
 > never seem any files with a space immediately after '>'. Although I don't
 > object to relaxing this a little in bioperl, you may find that these files
 > are not compatible with other software.

Yeah, there is that.  On the other hand, then we should make the
equivalent change and have the Bio::SeqIO object fail on them even if
it's told that they're Fasta (e.g. by -format or by guessing based on

I was just frustrated when stuff worked up until the moment that I
uploaded the file into a tool via the web (at which point it ended up
in an oddly named file and the guessing heuristic broke).

I'd vote for relaxing the constraint, but, hey....


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