[Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank to EMBL format

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2234


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |




------- Comment #2 from gwaldon at geneinfinity.org  2007-03-14 14:12 EST -------
Thanks Richard for the fix, but it seems that other problems were uncovered.
First doing the read/write/read operation with EMBL format only, I got "Bad ID
line found":
ID   AY847516; linear; mRNA; STD; HUM; 362 BP.

I added the version by hand:
ID   AY847516; SV 1; linear; mRNA; STD; HUM; 362 BP.
and I got "Current bioentry already has a version".

I removed the SV line, and I got "Bad date line found...",which corresponds to
the following line:
DT   01-JUN-2005 (Rel. 84 Created)

Finally, I added a coma after 84, and the file finally parsed without error.

In the process, I noticed that the first reference lost the last character of
the last RT line (missing 's' at the end of lymphocytes); note that the second
reference does not have RT lines.

Secondly, doing the read/write/read operation from Genbank to EMBL format, I
got similar progression; the bad date line has now a 0 instead of 84, but
adding the coma after 0 resolved the reading problem. Then I got a new error:
"Could not read sequence For input string: "GI:61815557", which is generated by
the following FT line:
FT                   /db_xref="taxon:GI:61815557"
I did not investigate further at this point.

I noticed that the above reference is now complete, but is incomplete when I do
the read/write/read operation from EMBL to Genbank. Therefore, this is probably
a read problem in the EMBL parser.


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