mapLoopLoci

Apply conservation class labels to loop loci mapped across species and/or cell types.

Map loop loci, in bedpe format, across cells and/or species. Input loops are labelled according to whether they are conserved (i.e., left and right anchors in the query both map to left and right anchors in the same target loop, allowing for possible inversions), partially conserved (one anchor is used in both species/cells), or species/cell-specific (neither anchor is used in the other species). Cross-species mappings are performed using the bnMapper algorithm, to map features from the target species to the query species of a chain alignment file.

Usage

mapLoopLoci.py [-h] [-s] [-o FILE] [-t FLOAT] [-g GAP] [-v {info,debug,silent}] [-k] [-m MIN_OVERLAP] [-w SLOP] query target alignment

Positional Arguments

Argument	Description
query	Input loops for the query species/cell.
target	Input loops for the target species/cell.
alignment	Alignment file (.chain or .pkl) (Ignored if using -s)

Optional Arguments

Short option	Long option	Argument Type	Description
-h	--help		Show help message and exit.
-s	--same_species		Query and target loops are from the same species. Cross-species mapping step will be skipped. (default: False)
-o	--output	FILE	Output file. Mandatory if more than on file in input. (default: stdout)
-t	--threshold	FLOAT	Mapping threshold i.e., (elem * threshold) <= (mapped_elem) (default: 0.0)
-g	--gap	INT	Ignore elements with an insertion/deletion of this or bigger size. (default: -1 -- accept all gapped alignments)
-v	--verbose	{info,debug,silent}	Verbosity level (default: info)
-k	--drop_split		If elements span multiple chains, silently drop instead of reporting the segment with the longest overlap. (This is the default behavior for bnMapper.) (default: False)
-m	--min_overlap	INT	Minimum amount of overlap to consider a pair of query/target anchors as shared. (default: 1)
-w	--slop	INT	Number of bases added up/downstream of query and target regions to enable flexible mapping. (default: 0)

Output

Column(s)	Description
1-9	Input BEDPE fields
10-13	Orthologous coordinates of the LEFT anchor in the target genome. (chrom, start, end, strand)
14-17	Orthologous coordinates of the RIGHT anchor in the target genome. (chrom, start, end, strand)
18-22	Target loop anchor overlapping LEFT anchor of query loop. (name, anchor_in_target ("l"eft/"r"ight), chrom, start, end)
23-27	Target loop anchor overlapping RIGHT anchor of query loop. (name, anchor_in_target ("l"eft/"r"ight), chrom, start, end)
28	Conservation class assignment.

Conservation classes

Class	Description
C	Conserved. Both anchors map and are assigned to the same target loop.
B2	Both anchors map, but are assigned to different target loops.
B1	Both anchors map, but only one is assigned to a target loop.
B0	Both anchors map, but neither is assigned to a target loop.
N1A	Semi-species-specific. Only one anchor maps to the target genome and the mapped anchor is used in target as a loop anchor.
N1B	Species-specific, semi-mapping. Only one anchor maps to the target genome and the mapped anchor is not used in target as a loop anchor.
N0	Species-specific, non-mapping. Neither anchor maps to the target genome.