[Bioperl-l] EMBL file with no feature table

Brian Osborne brian_osborne at cognia.com
Thu May 6 14:44:45 EDT 2004


Thank you for reporting this. What would also be helpful would be submitting
this as a bug (http://bugzilla.bioperl.org/), this way we won't lose track
of it.

Another note, not really directed at you or this module, and this is only my
personal opinion. Some of our modules are not really maintained, despite the
fact that most of them contain a "Maintained by ..." line. If when you see a
bug you actually know how to fix it, or are willing to put in that extra
effort to find the fix, please do so and tell us how it's done. We do have a
backlog of bugs that need to be addressed, some of them serious, and any
effort towards this end is much appreciated.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Eric Just
Sent: Thursday, May 06, 2004 2:20 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] EMBL file with no feature table

I have had a problem with the embl parser.  I got some EMBL files that did
not have a feature table, just sequence and it seems that the parser
requires a feature table:

        # Exit at start of Feature table
        last if /^F[HT]/;

if there is no feature table and it goes right to the SQ section (I THINK
that's allowed in EMBL) then you have to exit when you hit the SQ
line.  You need to then do a pushback when you exit this loop in order to
catch the SQ line later in the code

        last if /^(F[HT])|(SQ)/;




Eric Just
e-just at northwestern.edu
dictyBase Programmer
Center for Genetic Medicine
Northwestern University


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