Provided by: genometools_1.5.1-2ubuntu1_amd64
gt-uniq - Filter out repeated feature node graphs in a sorted GFF3 file.
gt uniq [option ...] [GFF3_file]
-v be verbose (default: no) -o redirect output to specified file (default: undefined) -gzip write gzip compressed output file (default: no) -bzip2 write bzip2 compressed output file (default: no) -force force writing to output file (default: no) -help display help and exit -version display version information and exit
A depth-first traversal of a feature node graph starts at the top-level feature node (or pseudo-node) and explores as far along each branch as possible before backtracking. Let’s assume that the feature nodes are stored in a list in the order of their traversal (called the “feature node list”). Two feature node graphs are considered to be repeated if their feature node lis t (from the depth-first traversal) have the same length and each feature node pai r (from both lists at the same position) is “similar”. Two feature nodes are “similar”, if they have the same sequence ID, feature type, range, strand, and phase. For such a repeated feature node graph the one with the higher score (of the top-level feature) is kept. If only one of the feature node graphs has a define d score, this one is kept.
Report bugs to <email@example.com>. 10/07/2012 GT-UNIQ(1)