odgi extract
Extract subgraphs or parts of a graph defined by query criteria.
SYNOPSIS
odgi extract [-f, --input-graphs=FILE] [-o, --out=FILE] [OPTION]…
DESCRIPTION
The odgi extract command extracts parts of the graph defined by query criteria.
OPTIONS
MANDATORY OPTIONS
-i, --idx=FILE
Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!
Graph Files IO
-o, --out=FILE
Store all subgraphs in this FILE. The file name usually ends with
.og.
Extract Options
-s, --split-subgraphs
Instead of writing the target subgraphs into a single graph, write one
subgraph per given target to a separate file named
path:start-end.og (0-based coordinates).-I, --inverse
Extract the parts of the graph that do not meet the query criteria.
-l, --node-list=FILE
A file with one node id per line. The node specified will be extracted
from the input graph.
-n, --node=ID
Specify a single node ID from which to begin our traversal.
-c, --context-steps=N
The number of steps (nodes) N away from our initial subgraph that we should
collect [default: 0 (disabled)].
-L, --context-bases
The number of bases N away from our initial subgraph that we should collect [default: 0 (disabled)].
-r, --path-range
Find the node(s) in the specified path range TARGET=path[:pos1[-pos2]]
(0-based coordinates).
-b, --bed-file=FILE
Find the node(s) in the path range(s) specified in the given BED FILE
-q, --pangenomic-range=FILE
Find the node(s) in the specified pangenomic range pos1-pos2 (0-based coordinates). The nucleotide positions refer to the pangenome’s sequence (i.e., the sequence obtained arranging all the graph’s node from left to right).
-E, --full-range
Collects all nodes in the sorted order of the graph in the min and max
position touched by the given path ranges. This ensures that all the paths of the subgraph are not split by node, but that the nodes are laced together again. Comparable to -R, --lace-paths=FILE, but specifically for all paths in the resulting subgraph. Be careful to use it with
very complex graphs.
-p, --paths-to-extract=FILE
List of paths to keep in the extracted graph. The FILE must contain one
path name per line and a subset of all paths can be specified.
Paths specified in the input path ranges (with
-r/--path-range and/or -b/--bed-file)
will be kept in any case.-R, --lace-paths=FILE
List of paths to fully retain in the extracted graph. Must contain one
path name per line and a subset of all paths can be specified.
-d, --max-distance-subpaths=N
Maximum distance between subpaths allowed for merging them.
It reduces the fragmentation of unspecified paths in the input path ranges.
Set 0 to disable it.
-e, --max-merging-iterations=N
Maximum number of iterations in attempting to merge close subpaths.
It stops early if during an iteration no subpaths were merged [default: 3].
Threading
-t, --threads=N
Number of threads to use for parallel operations.
Processing Information
-P, --progress
Print information about the operations and the progress to stderr.
Program Information
-h, --help
Print a help message for odgi extract.