+
+=pod
+
+=head1 NAME
+
+gff2annot.pl
+
+=head2 SYNOPSIS
+
+
+ gff2annot.pl [one or more files containing gff annotation]
+
+Generates a nominally usable Jalview Annotation file on B<STDOUT> from arbitrary GFF annotation lines.
+
+=head2 DESCRIPTION
+
+This script will generate a jalview features file on standard out, from a set of GFF annotation lines input from STDIN and/or any provided filenames.
+
+For a series of GFF annotation lines looking like :
+
+E<lt>seqIdE<gt> E<lt>sourceE<gt> E<lt>nameE<gt> E<lt>startE<gt> E<lt>endE<gt> [E<lt>scoreE<gt> E<lt>strandE<gt> E<lt>frameE<gt> [E<lt>AttributeE<gt> E<lt>Attribute-Value<gt>]]
+
+The script will generate a seuqence features file on B<STDOUT> where annotation with a particular B<source> string will be grouped together under that name.
+
+=head2 Example
+
+Passing some GFF annotation through STDIN:
+
+ perl gff2annot.pl
+ Seq1 blastx significant_hsp 1 5 0.9 + 1 link http://mylink/
+ # a comment
+ Seq1 blasty significant_hsp 15 25 0.9 + 1 link http://mylink/
+ Seq1 blastz significant_hsp 32 43 0.9 + 1 link http://mylink/
+ Seq2 blastx significant_hsp 1 5 0.9 + 1 link http://mylink/
+ Seq2 blasty significant_hsp 1 5 0.9 + 1 link http://mylink/
+ Seq2 blastz significant_hsp 1 5 0.9
+ Seq3 blastx significant_hsp 50 70
+ <Control^D/Z>
+
+Produces
+
+ significant_hsp FF0000
+ STARTGROUP blasty
+ significant_hsp Seq1 -1 15 25 significant_hsp
+ significant_hsp Seq2 -1 1 5 significant_hsp
+ ENDGROUP blasty
+ STARTGROUP blastx
+ significant_hsp Seq1 -1 1 5 significant_hsp
+ significant_hsp Seq2 -1 1 5 significant_hsp
+ significant_hsp Seq3 -1 50 70 significant_hsp
+ ENDGROUP blastx
+ STARTGROUP blastz
+ significant_hsp Seq1 -1 32 43 significant_hsp
+ significant_hsp Seq2 -1 1 5 significant_hsp
+ ENDGROUP blastz
+
+=cut