Hi Lionel,
if I find some time I'll test it as well.
We have even phd.ball of almost 30G(!), for more or less historical
reasons, as consed supports loading more than one phd.ball since v17
AFAIK. We started using phd.balls quite ealier (we also wrote our
own predPhrap), because we were not able to (effeciently) handle
400,000 or more single phd files in a single filesystem ..
You should think about distinguishing sanger and 454 data, as for
454 data you probably can
omit the follwing tags:
CALL_METHOD:
QUALITY_LEVELS:
I'd also think about adding real chromatogram names to the phd.ball
as only this option lets you edit single reads (and thus lets you
changing consensus) ...
If you do so, you need to calculate the peak positions as well.
$peakpos = (++$basepos - 1)*19 + 15;
just some thoughts,
Sven
2009/10/23 Lionel Guy <guy.lionel@xxxxxxxxx>
Hi there,
Following my yesterday's message, I changed my original idea and
finally
parsed the mira-produced caf file to obtain a phd.ball file to be used
with consed. The idea behind that is to have qualities associated with
reads when editing mira assemblies within consed. This is very
important
for example when merging/tearing contigs, because the consensus is
recalculated in a very, very bad way if you don't have qualities
(especially because mira doesn't physically trims the reads from the
vector sequences...).
The result is a small perl script that works for my data, but I
would be
glad if others could test it to see if it works with other types of
data. All comments are welcome!
CAVEAT: this script produces huuuuge files, because it writes one line
per base, plus headers. For example, I have 350'000 reads and some
long
Sanger, and I get a file which is 1.4 Gb...
Cheers,
Lionel
