Hi - I did this once for an EMBL contig file. From memory I called the file EMBLAssemble :) The only problem is that you have to make available all the other Genbank or EMBL records that are referenced. I also found quite a few errors in the syntax of the join statements which indicates to me that they where not well used in those days.
- Mark -----Original Message----- From: Matthew Pocock [mailto:[EMAIL PROTECTED] Sent: Fri 27/06/2003 6:57 a.m. To: Matthew Pocock Cc: biojava-l Subject: [Biojava-l] Re: genbank contig stuff Sory - I fired that off without thinking much. I just downloaded the genbank file NT_010783 from the ncbi. Our parsers spewed lots of errors about features not being within the range 1..0, and after a little poking arround in the code, I found that a zero length sequence was being generated. In despiration, I looked at the physical genbank file. Instead of sequences, it contains a CONTIG section with a single big join() describing how to build it from other entries. Has anybody modified our genbank parser to process entries like this? To be honest, I'm not quite sure where to start. Matthew _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
