From: Scott C. <sco...@us...> - 2005-06-29 17:21:07
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Update of /cvsroot/gmod/schema/chado/load/bin In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8217 Modified Files: bulk_load_gff3.PLS Log Message: adding documentation about sequence-region non-handling Index: bulk_load_gff3.PLS =================================================================== RCS file: /cvsroot/gmod/schema/chado/load/bin/bulk_load_gff3.PLS,v retrieving revision 1.38 retrieving revision 1.39 diff -C2 -d -r1.38 -r1.39 *** bulk_load_gff3.PLS 16 Jun 2005 17:48:56 -0000 1.38 --- bulk_load_gff3.PLS 29 Jun 2005 17:20:58 -0000 1.39 *************** *** 81,84 **** --- 81,98 ---- accession numbers may be supported in future versions of this script). + Note that the ##sequence-region directive is not supported as a way of + declaring a reference sequence for a GFF3 file. The ##sequence-region + directive is not expressive enough to define what type of thing the + sequence is (ie, is it a chromosome, a contig, an arm, etc?). If + your GFF file uses a ##sequence-region directive in this way, you + must convert it to a full GFF3 line. For example, if you have + this line: + + ##sequence-region chrI 1 9999999 + + Then is should be converted to a GFF3 line like this: + + chrI . chromosome 1 9999999 . . . ID=chrI + =head2 How GFF3 is stored in chado |