From: <sco...@us...> - 2004-01-07 14:47:12
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Update of /cvsroot/gmod/schema/chado/load/bin In directory sc8-pr-cvs1:/tmp/cvs-serv25544/load/bin Modified Files: load_gff3.PLS Log Message: documentation updates Index: load_gff3.PLS =================================================================== RCS file: /cvsroot/gmod/schema/chado/load/bin/load_gff3.PLS,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** load_gff3.PLS 6 Jan 2004 23:04:13 -0000 1.14 --- load_gff3.PLS 7 Jan 2004 14:47:09 -0000 1.15 *************** *** 27,39 **** =head1 NAME ! load_gff3.pl - Load gff3 files into a chado database. =head1 SYNOPSIS ! % load_gff3.pl --organism Human --srcdb 'DB:refseq' --gfffile refseq.gff =head1 DESCRIPTION ! See the notes; there is plenty there. =head2 NOTES --- 27,57 ---- =head1 NAME ! gmod_load_gff3.pl - Load gff3 files into a chado database. =head1 SYNOPSIS ! % gmod_load_gff3.pl --organism Human --srcdb 'DB:refseq' --gfffile refseq.gff =head1 DESCRIPTION ! The gmod_load_gff3.pl script takes genomic annotations in the GFF3 format ! and loads them into several tables in chado. (see ! L<http://song.sourceforge.net/gff3.shtml> for a description of the format). ! There are two types of data tags in GFF3: those that are part of the ! specification, and those that aren't. There is a short list of those that ! are part of the spec (ie, reserved) They include ID, Parent, Name, Alias, ! Target, and Gap. Tags that are part of the spec are first letter capitalized ! and all other tags are all lower case. All tags that are part of the spec ! are handled as special cases during the insert, as well as some non-spec ! tags. These include 'description', tags beginning with 'db:' or 'DB:', ! and tags beginning with 'cvterm:'. All other tags are inserted into the ! same table (featureprop). If that is not the desired behavior for a given ! tag, you may look at modifying the load_custom_tags subroutine. If you ! have a modification that you feel might be particularly useful, please ! email your suggestion to the authors. ! ! (Note that this behavior might better be module-ized, so that we could ! provide an empty 'custom tag processing' module, that if installed, would ! provide addtional processing of custom tags. Add it to the todo list.) =head2 NOTES *************** *** 255,261 **** --- 273,288 ---- print "\n$seqs_loaded sequences added\n"; print "Done\n"; + exit 0; + =pod + =head1 load_custom_tags + Handles inserting non-reserved tags into chado. Determines if the tag + falls into a short list of tags for custom handling and deals with them + appropriately. If the tag is not on the list, the information is placed + in the featureprop table. + + =cut sub load_custom_tags { *************** *** 350,353 **** --- 377,388 ---- } + =pod + + =head1 load_ID_tag + + Loads ID tag values + + =cut + sub load_ID_tag { my $gff_feature = shift; *************** *** 381,384 **** --- 416,427 ---- } + =pod + + =head1 load_Note_tag + + Loads Note tag values to the featureprop table. + + =cut + sub load_Note_tag { my $gff_feature = shift; *************** *** 400,403 **** --- 443,456 ---- } + + =pod + + =head1 load_Target_tag + + Loads Target values. These are used for alignment information. + + =cut + + sub load_Target_tag { my $gff_feature = shift; *************** *** 448,451 **** --- 501,514 ---- } + =pod + + =head1 load_Parent_tag + + Loads Parent tag values. These are used to denote a parent feature + of the given feature. + + =cut + + sub load_Parent_tag { my $gff_feature = shift; *************** *** 471,474 **** --- 534,546 ---- } + =pod + + =head1 load_Alias_tag + + Loads Alias tag values. These are used for synonyms. + + =cut + + sub load_Alias_tag { my $gff_feature = shift; *************** *** 497,500 **** --- 569,581 ---- } } + + =pod + + =head1 load_Name_tag + + Loads Name tag values. + + =cut + sub load_Name_tag { |