The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

glyparse

Parse different glycan structure text nomenclature into glyrepr::glycan_structure.

Currently, the following formats are supported: IUPAC-extended, IUPAC-condensed, IUPAC-short, WURCS, GlycoCT, StrucGP-style, pGlyco-style.

Installation

You can install the latest release of glyparse from CRAN with:

install.packages("glyparse")

Or install the development version from GitHub:

remotes::install_github("glycoverse/glyparse")

Documentation

• 📚 Reference: Here

Role in glycoverse

While glyrepr natively supports parsing IUPAC-condensed format through as_glycan_structure(), the glycan community has developed numerous other nomenclature formats that remain widely adopted in different contexts. glyparse serves as a comprehensive extension to glyrepr, providing robust parsing capabilities for these diverse formats. The package can be utilized directly by researchers to parse glycan structure text strings, or integrated with other packages such as glyread to seamlessly handle structure parsing when processing results from glycan and glycopeptide analysis software.

Example

library(glyparse)

# Parse a StrucGP-style structure string
parse_strucgp_struc("A2B2C1D1E2F1fedD1E2edcbB5ba")
#> <glycan_structure[1]>
#> [1] Hex(??-?)HexNAc(??-?)Hex(??-?)[HexNAc(??-?)Hex(??-?)]Hex(??-?)HexNAc(??-?)[dHex(??-?)]HexNAc(??-
#> # Unique structures: 1

# Parse a pGlyco-style structure string
parse_pglyco_struc("(N(F)(N(H(H(N))(H(N(H))))))")
#> <glycan_structure[1]>
#> [1] Hex(??-?)HexNAc(??-?)Hex(??-?)[HexNAc(??-?)Hex(??-?)]Hex(??-?)HexNAc(??-?)[dHex(??-?)]HexNAc(??-
#> # Unique structures: 1

# Parse a condensed IUPAC structure string
parse_iupac_condensed("Gal(b1-3)GlcNAc(b1-4)Glc(a1-")
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GlcNAc(b1-4)Glc(a1-
#> # Unique structures: 1

# Parse a WURCS structure string
parse_wurcs("WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1")
#> <glycan_structure[1]>
#> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> # Unique structures: 1

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.