Hello,
I've been working on using Bio.Sequence.Phd to read some .phd files.
When I load up the module in ghci and try to apply readPhd to a .phd
file, I keep getting an error that says:
*** Exception: failed to parse quality value
I've tried making a few simple .phd files by hand, and they can be read
without error.
I've also tried stripping all of the tags off the end of my real .phd
files, which allows them to be read without error as well. The tags
that I'm talking about look like this:
BEGIN_DNA
.
.
.
t 6 16242
c 6 16260
a 6 16261
t 8 16281
t 6 16289
END_DNA
WR{
template determineReadTypes 110211:141953
name: 001_PEN
lib: CG02601
type: pcr
}
WR{
primer determineReadTypes 110211:141953
type: univ fwd
}
BEGIN_TAG
TYPE: homozygoteAA
SOURCE: polyPhred
UNPADDED_READ_POS: 67 67
DATE: 02/11/11 15:58:10
END_TAG
BEGIN_TAG
TYPE: homozygoteGG
SOURCE: polyPhred
UNPADDED_READ_POS: 77 77
DATE: 02/11/11 15:58:10
END_TAG
I've noticed that in the Bio.Sequence.Phd source, there is a short note
about adding checking for "BEGIN_DNA and END_DNA."
Can anyone give me some hints on how I or someone else can patch up the
code, just so that it doesn't fail when those tags are present?
Eventually it would be nice if the tags could be read too but I think
that can wait for another email.
Thanks,
Dan
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