[BiO BB] gff to sequence

Mike Marchywka marchywka at hotmail.com
Sat Oct 3 19:06:05 EDT 2009

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> This seems of such general use that it begs a small utility which will
> take a (possibly indexed) fasta file=2C a gff and output the sequences yo=
> want. What would people want from such a programme?
> Is GTF (http://mblab.wustl.edu/GTF2.html) more useful or GFF?
> Would different elements from the same group (gene/transcript) be joined
> together in order?

I wrote a small system like this based on ASCII hit files-
this means most of your temp files can be processed with
standard tools and usually they don't limit the speed although
with cygwin going through windoze this can add up.=20

> Would one want filtering on the "features" column so one could retrieve a=
> splice sites or codon exons?
> What would be the output? Another fasta file? How would each "group" of
> Sequences (e.g. transcript) be labelled? By a user supplied regular expre=
>> I guess it depends what you mean by quick- quick to write you could use =
>> but then it depends what additional things you want to do with results.=
>> I ended up writing a C++ fasta utility program since PERL can slow down =
>> etimes but I ended up grabbing a couple of regex libraries to let me=3D2=
>> grep names etc.=3D20
> I hoped you used boost:regex which will be in the next c++ standard

If you had to read my posts on their mail list youwould change your attitud=
and wish I never heard of it:) Actually=2C as pointed out there=2C it
isn't clear how fast it is compared to greta ( for all my complaints
on msft that works well but maddock is at boost in any case). Finally
I wrote my own limited compiler but there seem to be boost expression
compilers that may be useful too. For editing fasta files=2C I doubt you
care this much about regex speed however.=20

Note: hotmail is now unusable for TEXT=2C I am moving to marchywka at gmail.co=
m or also use
marchywka at yahoo.com. Thanks.

Mike Marchywka
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