If we agreed on migrating the code to Biojava3, I can do it.
especially as I haven't done something useful on the group for a while.
Amr
--------------------------------------------------
From: "Scooter Willis" <[email protected]>
Sent: Friday, July 29, 2011 3:11 AM
To: "Trent Schafer" <[email protected]>; "[email protected]"
<[email protected]>
Subject: Re: [Biojava-l] ab1 files
Trent
We do not have support for AB1 files in Biojava3. Do you have any interest
in working/migrating the code for the AB1 file parser? I can assist if you
want to work on it.
Scooter
On 7/28/11 7:32 PM, "Trent Schafer" <[email protected]> wrote:
Hi,
Not sure if anyone can help or advise - still just trying to figure it
out.
We are using this database software to manage our clinical studies, and we
want to add the functionality to store sequencing files, and hopefully
some
useful information extracted from the files we upload.
I found in the legacy cookbooks the following:
http://biojava.org/wiki/BioJava:Cookbook:SeqIO:ABItoSequence and based on
an
AB1 file I have on my workstation, was able to successfully run the code
listed - I presume its also possible to extract the quality scores?
Anyway, was trying to see if these files can be read in BioJava 3.x?
I was trying the 2 examples listed here:
http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite but the
exception is thrown: Exception in thread "main"
org.biojava3.core.exceptions.CompoundNotFoundError: Compound not found
for:
Cannot find compound for:
So my assumption is that it just doesn't know how to read AB1 files?
To summarise, is it only possible read AB1 files in the legacy version of
the software? I assume its better to be using 3.x if possible? There is a
section of the 3.x cookbook:
http://biojava.org/wiki/BioJava:CookBook:Core:Sequences is it that this
hasn't been implemented yet, or is just undocumented?
Any information is much appreciated.
Thx,
Trent
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