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GT-UNIQ(1) | GenomeTools Manual | GT-UNIQ(1) |
NAME¶
gt-uniq - Filter out repeated feature node graphs in a sorted GFF3 file.SYNOPSIS¶
gt uniq [option ...] [GFF3_file]DESCRIPTION¶
-v [yes|no]be verbose (default: no)
-o [filename]
redirect output to specified file (default:
undefined)
-gzip [yes|no]
write gzip compressed output file (default: no)
-bzip2 [yes|no]
write bzip2 compressed output file (default: no)
-force [yes|no]
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 list
(from the depth-first traversal) have the same length and each feature node
pair (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
defined score, this one is kept.
REPORTING BUGS¶
Report bugs to <gt-users@genometools.org>.07/29/2016 | GenomeTools 1.5.9 |