parse_uc: Parse UC files (clustering output from USEARCH, VSEARCH,...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Parse UC files (clustering output from USEARCH, VSEARCH, SWARM)

Description

Parse UC files (clustering output from USEARCH, VSEARCH, SWARM)

Usage

parse_uc(x, map_only = F, package = "data.table", rm_dups = TRUE)

Arguments

x	File name (typically with .uc extension)
map_only	Logical, return only mapping (correspondence of query and cluster)
package	Which package to use ("base" or "data.table")
rm_dups	Logical, remove duplicated entries (default, TRUE)

Details

USEARCH cluster format (UC) is a tab-separated text file. Description of the UC file format (from USEARCH web-site: http://www.drive5.com/usearch/manual/opt_uc.html): 1 Record type S, H, C or N (see table below). 2 Cluster number (0-based). 3 Sequence length (S, N and H) or cluster size (C). 4 For H records, percent identity with target. 5 For H records, the strand: + or - for nucleotides, . for proteins. 6 Not used, parsers should ignore this field. Included for backwards compatibility. 7 Not used, parsers should ignore this field. Included for backwards compatibility. 8 Compressed alignment or the symbol '=' (equals sign). The = indicates that the query is 100 9 Label of query sequence (always present). 10 Label of target sequence (H records only).

Record Description H Hit. Represents a query-target alignment. For clustering, indicates the cluster assignment for the query. If ‑maxaccepts > 1, only there is only one H record giving the best hit. To get the other accepts, use another type of output file, or use the ‑uc_allhits option (requires version 6.0.217 or later). S Centroid (clustering only). There is one S record for each cluster, this gives the centroid (representative) sequence label in the 9th field. Redundant with the C record; provided for backwards compatibility. C Cluster record (clustering only). The 3rd field is set to the cluster size (number of sequences in the cluster) and the 9th field is set to the label of the centroid sequence. N No hit (for database search without clustering only). Indicates that no accepts were found. In the case of clustering, a query with no hits becomes the centroid of a new cluster and generates an S record instead of an N record.

Value

Data.frame or data.table.

References

http://www.drive5.com/usearch/manual/opt_uc.html

Examples

parse_uc("usearch_OTUs.uc", map_only = F)
parse_uc("usearch_OTUs.uc", map_only = T)

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.