v1.6.3

Changelog

[1.6.3]

• glycowork is now compatible with specifying narrow modification ambiguities (e.g., Gal(b1-3)GalNAc4/6S) (ec290e8)
• made the bokeh dependency runtime-optional by importing it just-in-time for plot_network (ea9929e)

glycan_data

stats

Added ✨

• Alpha biodiversity calculation in alpha_biodiversity_stats now performs Welch's ANOVA instead of ANOVA if scipy>=1.16 (ab73368)
• ALR transformation functions now also expose the random_state keyword argument for reproducible seeding (23cafe7)

motif

processing

Added ✨

• COMMON_ENANTIOMER dict to track the implicit enantiomer state (e.g., we write Gal instead of D-Gal but we do note the deviation L-Gal) (bb7575c)
• GLYCONNECT_TO_GLYTOUCAN dict to support GlyConnect IDs as input to Universal Input / canonicalize_iupac (ea9929e)

Changed 🔄

• canonicalize_iupac and its parsers will now leave the D-/L- prefixes in monosaccharides, which will then be centrally homogenized with COMMON_ENANTIOMER, for a more refined and detailed output (bb7575c)
• canonicalize_iupac now considers more IUPAC variations, such as Neu5,9Ac instead of Neu5,9Ac2 (a764897)
• canonicalize_iupac no longer strips trailing -Cer (d8c948b)
• canonicalize_iupac now handles alpha and beta (d8c948b)
• glycoworkbench_to_iupac is now trigged by presence of either End-- or u-- (d8c948b)
• wurcs_to_iupac now supports more tokens (d9d6e57)
• canonicalize_iupac now supports Gal4,6Pyr modifications (487c68a)
• wurcs_to_iupac can now process sulfur linkages (e.g., Glc(b1-S-4)Glc) (88b2d54)
• wurcs_to_iupac is now more robust to prefixes (e.g., L-, 6-deoxy-, etc) (ac171c5)
• wurcs_to_iupac can now deal with ultra-long glycans (i.e., a-z, A-Z, aa-az, and aA-aZ) (487c68a)

tokenization

Changed 🔄

• glycan_to_composition is now compatible with the new narrow modification ambiguities (e.g., Gal(b1-3)GalNAc4/6S) (ec290e8)

graph

Changed 🔄

• compare_glycans is now compatible with the new narrow modification ambiguities (e.g., Gal(b1-3)GalNAc4/6S) (ec290e8)

draw

Fixed 🐛

• fixed overlap in floating substituents in GlycoDraw if glycan had fewer branching levels than unique floating substituents (daade78)

analysis

Added ✨

• ANOVA-based time series analysis in get_time_series now performs Welch's ANOVA instead of ANOVA if scipy>=1.16 (ab73368)
• All analysis endpoint functions can now be directly seeded, without having to pre-transform data, with the newly exposed random_state keyword argument (23cafe7)