[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
filename).

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....

g.


More information about the Bioperl-l mailing list