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Changelog

[1.5.0]

Added ✨

  • Added type hints to all functions (e6721a1)
  • Added CodeCov shield to track PyTest test code coverage (23d6456)
  • Added more PyTest unit tests (e.g., 0c94995, 23d6456, 5a99d6b, f76535e, 94646ad, d5f5d4e, 918d18f, d1a8c6d, 194f31c)
  • Added setuptools to required_installs to support pip installation beyond pip 25.0 (94646ad)
  • Added pyproject.toml to support pip installation beyond pip 25.0 (94646ad)
  • Added CITATION.bib to allow for even easier citation of glycowork (a64f694)
  • Reworked user interface of the glycoworkGUI (77bbfa3)

Changed 🔄

glycan_data

Added ✨
  • Added new named motifs to motif_list: DisialylLewisC, Sia(a2-3)Gal(b1-3)[Sia(a2-6)]GlcNAc; RM2, Sia(a2-3)[GalNAc(b1-4)]Gal(b1-3)[Sia(a2-6)]GlcNAc; DisialylLewisA, Sia(a2-3)Gal(b1-3)[Fuc(a1-4)][Sia(a2-6)]GlcNAc (a64f694)
  • Added new curated glycomics dataset, mouse_brain_GSL_PMID39375371 (b94744e)
Changed 🔄
  • Changed glycoproteomics_human_keratinocytes_PMID37956981 to glycoproteomics_human_keratinocytes_N_PMID37956981 (d5f5d4e)
  • Improved the description of blood group motifs in motif_list (including type 3 blood group antigens, ExtB, and parent motifs) (b94744e)
Fixed 🐛
  • Fixed the "Oglycan_core6" motif definition in motif_list to no longer overlap with core 2 structures (f394bda)

loader

Added ✨
  • Added count_nested_brackets helper function to monitor level of nesting in glycans (41bb1a1, d57b836)
  • Added dictionaries with lists of strings as values as a new supported data type for DataFrameSerializer (034b6ad)
  • Added share_neighbor helper function to check whether two nodes in a glycan graph share a neighbor (f394bda)
Changed 🔄
  • Changed resources.open_text to resources.files to prevent DeprecationWarning from importlib (0c94995)
  • lectin_specificity now uses our custom DataFrameSerializer and is stored as a .json file rather than a .pkl file, to improve long-term stability across versions (034b6ad)
Fixed 🐛
  • Fixed DeprecationWarning in all data-loading functions that used importlib.resources.open_text or .content (87ea2fc)

stats

Added ✨
  • Added the "random_state" keyword argument to clr_transformation to allow users to provide a reproducible RNG seed (b94744e)
  • Added the JTKTest class object (87ea2fc)
Changed 🔄
  • For replace_outliers_winsorization, in small datasets, the 5% limit is dynamically changed to include at least one datapoint (23d6456)
  • Handled the edge case of strong differences in cohen_d with zero standard deviation; now outputting positive/negative infinity (23d6456)
  • Renamed test_inter_vs_intra_group to compare_inter_vs_intra_group, to avoid testing issues (23d6456)
  • partial_corr will now return a normal Spearman's correlation if no control features can be identified (241141b)
Deprecated ⚠️
  • Deprecated hlm, fast_two_sum, two_sum, expansion_sum, and update_cf_for_m_n, which will all be done in-line instead (e1afe33)
  • Deprecated jtkdist, jtkinit, jtkstat, jtkx, which will all be done by the new JTKTest (87ea2fc)
Fixed 🐛
  • Fixed DeprecationWarning in calculate_permanova_stat for calling nonzero on 0d arrays (23d6456)
  • Prevent possible division by zero in pseudo-F calculation in calculate_permanova_stat (23d6456)
  • Fixed DeprecationWarning in jtkdist for calling np.sum(generator) (23d6456)
  • Ensured that the input to impute_and_normalize are columns with floats, to avoid TypeWarnings during imputation (23d6456)
  • Fixed DeprecationWarning in process_glm_results to prevent DataFrameGroupBy.apply from operating on the grouping columns (23d6456)
  • Fixed RuntimeWarnings for JTK-related functions in case of imperfect input data (d5f5d4e)
  • Ensured that correct_multiple_testing will return empty lists if the provided p-value list is also empty (ef3da9c)

motif

tokenization

Added ✨
  • Added get_random_glycan to retrieve random glycan sequences (optionally of specific glycan type) (d1a8c6d)
  • Supported intramolecular modifications like lactonization in glycan_to_composition (8c69c2c)
Changed 🔄
  • Changed resources.open_text to resources.files to prevent DeprecationWarning from importlib (0c94995)
  • The monosaccharide keys of the output dictionaries of glycan_to_composition are now alphabetically sorted (8c69c2c)
  • Modified calculate_adduct_mass to deal with a greater variety of adduct handling, such as "C2H4O2", "-H2O", "+Na" to add or subtract masses (8c69c2c)
  • Expanded glycan_to_mass and composition_to_mass to deal with compositional building blocks that represent losses/gains in the molecule (like "-H2O") (8c69c2c)
  • Composition and mass functions now can correctly work with azide-modified monosaccharides such as Neu5Az (ef3da9c)
  • In addition to chemical formulae, users can now also provide direct additional masses as floats with the same "adduct" keyword argument in composition_to_mass and glycan_to_mass (d57b836)
  • get_modification will no longer return the 5Ac / 5Gc of Neu5Ac / Neu5Gc as part of the modification (0387d37)
Fixed 🐛
  • Fixed an edge case in get_unique_topologies, in which the absence of a universal replacer sometimes created an empty list that was attempted to be indexed (0c94995)
  • Made sure that compositions_to_structures always returns a DataFrame, even if no matches are found (0c94995)
  • Provided correct exact methyl masses in mass_dict (e3eeb32)

processing

Added ✨
  • Added "antennary_Fuc" as another inferred feature to infer_features_from_composition (a64f694)
  • Added "IdoA", "GalA", "Araf", "D-Fuc", "AllNAc", "Par", "Kdo", "GlcN", "Ido", "Col", "Tyv", "GalN", "QuiNAc", "Gul", and "Gal6S" to recognized WURCS2 tokens (52fc16e, f3cd8f0, 7551805, 35ed71a)
  • Added the new "order_by" keyword argument to choose_correct_isoform to enforce strictly sorting branches by branch endings / linkages, if desired (918d18f)
  • Added "Col", "Ido", "Kdo", and "Gul" to supported GlycoCT monosaccharides (7551805, 35ed71a)
  • GLYCAM is now another supported nomenclature in the Universal Input framework, enabled by the added glycam_to_iupac function, which is also integrated into canonicalize_iupac (2fb5dc6)
  • GlycoWorkBench (GlycanBuilder) is now another supported nomenclature in the Universal Input framework, enabled by the added glycoworkbench_to_iupac function, which is also integrated into canonicalize_iupac (ea1fdfc)
Changed 🔄
  • check_nomenclature will now actually raise appropriate Exceptions, in case nomenclature is incompatible with glycowork, instead of print warnings (23d6456)
  • Supported triple-branch reordering in find_isomorphs and choose_correct_isoform (918d18f)
  • Improved find_isomorphs to swap neighboring branches with different levels of nesting (41bb1a1, 034b6ad)
  • choose_correct_isoform can now also be used with a single glycan sequence, in which case it internally calls find_isomorphs to generate material for choosing (918d18f)
  • choose_correct_isoform can now correctly handle more complex sequences than before (41bb1a1, 034b6ad, d1ff321)
  • canonicalize_iupac now can handle modifications such as Neu5,9Ac2 / Neu4,5Ac2 or multiple ones like in (6S)(4S)Gal, even if in the wrong order (034b6ad)
  • canonicalize_iupac now can handle even more typos (e.g., 'aa1-3' in specifying a linkage) (a64f694, 241141b)
  • canonicalize_iupac now can handle even more inconsistencies (e.g., mix of short-hand and expanded linkages)
  • Expanded get_mono to deal with some special WURCS2 tokens at the reducing end, of type u2122h_2*NCC/3=O (d57b836)
  • canonicalize_iupac will no longer convert things like "b1-3/4" into "b1-?", because narrow linkage ambiguities can now be properly handled (52fc16e)
  • get_possible_linkages and de_wildcard_glycoletter now also support narrow linkage ambiguities like "b1-3/4" (52fc16e)
  • canonicalize_iupac will now no longer mess up branch formatting of the repeating unit in glycans of type "repeat" (9a94537)
  • Ensured that canonicalize_iupac works with lactonized glycans (i.e., containing something like "1,7lactone") (8c69c2c)
  • find_matching_brackets_indices has been renamed to get_matching_indices and now takes multiple delimiter choices and returns a generator, including the level of nesting (basically what .draw.matches used to do) (e1afe33)
  • get_class will now return "lipid/free" if glycans of type Neu5Ac(a2-3)Gal(b1-4)Glc are supplied (i.e., lacking 1Cer and -ol but still lactose-core based) (b99699c)
  • expand_lib now no longer modifies the input dictionary (65bd12c)
  • get_possible_linkages now returns a set instead of a list (a98461f)
  • wurcs_to_iupac now can also properly deal with ultra-narrow linkage wildcards (e.g., a2-3/6) (f3cd8f0)
Fixed 🐛
  • Fixed component inference in parse_glycoform in case of unexpected composition formats (0c94995)
  • Fixed an issue in equal_repeats, in which identical repeats sometimes were not returning True (0c94995)

graph

Added ✨
  • Natively support narrow linkage ambiguity in categorical_node_match_wildcard; that means you can use things like "Gal(b1-3/4)GlcNAc" with subgraph_isomorphism or compare_glycans (as well as all functions using these core functions) and it will only return True for "Gal(b1-3)GlcNAc", "Gal(b1-4)GlcNAc", and "Gal(b1-?)GlcNAc" (b94744e)
  • Added build_wildcard_cache for a central handling of wildcard mapping that can also be cached (a98461f)
  • compare_glycans now also has the return_matches keyword argument that allows for a retrieval of the node mapping if the glycans are isomorphic (7c510c9)
Changed 🔄
  • Ensured that compare_glycans is 100% order-specific, never matching something like ("Gal(b1-4)GlcNAc", "GlcNAc(b1-4)Gal") (5a99d6b)
  • glycan_to_nxGraph will now return an empty graph if the input is an empty string (4f1ccfa)
  • get_possible_topologies will now also produce a warning (and return the input) if an already defined topology is provided as a pre-calculated graph (3f22f14)
  • Negation in subgraph_isomorphism can now also be added for internal monosaccharides (e.g., "Neu5Ac(a2-3)!Gal(b1-4)GlcNAc") (7558d9b)
  • Functions with the handle_negation decorator can now be accessed without the decorator via .__wrapped__ (7558d9b)
Fixed 🐛
  • Fixed an edge case in which subgraph_isomorphism could erroneously return False if any of the matchings were in the wrong order, if "count = False" (f394bda)
  • Fixed an edge case in which negated motifs in subgraph_isomorphism sometimes wrongly returned False because the negated motif was present somewhere else in the glycan (but the intended motif was still there) (7558d9b)

draw

Added ✨
  • Added the "drawing" argument to draw_hex, hex_circumference, add_bond, add_sugar, and draw_bracket to avoid having to operate on global variables (918d18f)
  • Added the option to provide your own existing glycan .pdb structures to GlycoDraw when using draw_method='chem3d' with the new keyword argument pdb_file (9d082a6)
Changed 🔄
  • matches can now also use [] as delimiters (f76535e)
  • Support easy import of GlycoDraw, via from glycowork import GlycoDraw (d5f5d4e)
  • Renamed hex to draw_hex, to avoid overwriting the built-in hex (918d18f)
  • Changed keyword argument "hex" to "hex_codes" in add_colours_to_map (838c708)
  • get_highlight_attribute now internally uses motif.graph.subgraph_isomorphism for pattern retrieval, ensuring up-to-date functionality (4f1ccfa)
  • get_coordinates_and_labels now internally uses motif.processing.choose_correct_isoform to reorder the glycan for drawing (41bb1a1)
  • Improved console drawing quality controlled by display_svg_with_matplotlib and image quality in Excel cells using plot_glycans_excel (a64f694)
  • draw_chem2d and draw_chem3d will now detect whether the user is in a Jupyter environment and, if not, plot to the Matplotlib console (c3a7f64)
  • process_per_residue now will re-order the per_residue list in the same way as the glycan is re-ordered for drawing with GlycoDraw (7c510c9)
Deprecated ⚠️
  • Deprecated hex_circumference, the functionality is now available within draw_hex with the new keyword argument "outline_only" (4f1ccfa)
  • Deprecated multiple_branches, multiple_branch_branches, branch_order, and reorder_for_drawing accordingly (41bb1a1)
  • Deprecated matches, which will now be done by .processing.get_matching_indices that has been reworked
Fixed 🐛
  • Made sure scale_in_range never divides by zero, if value range is zero (f76535e)
  • Made sure that monosaccharides that were never observed but are still SNFG-defined (like TalNAc vs 6dTalNAc) can still be drawn with GlycoDraw (ef24af4)

analysis

Changed 🔄
  • get_glycanova will now raise a ValueError if fewer than three groups are provided in the input data (f76535e)
  • Improved console drawing quality controlled by display_svg_with_matplotlib and image quality in Excel cells using plot_glycans_excel (a64f694)
  • The "periods" argument in get_jtk is now a keyword argument and has a default value of [12, 24] (87ea2fc)
  • specify_linkages can now also handle super-narrow linkage wildcards like Galb3/4 (f394bda)
  • get_SparCC will now limit the number of eligible controls for "partial_correlations=True" to sample_size//5, capped at 5 (241141b)
Fixed 🐛
  • Fixed a FutureWarning in get_lectin_array by avoiding DataFrame.groupby with axis=1 (f76535e)
  • Fixed a RuntimeWarning in get_biodiversity by handling statistical tests of identical alpha diversity values between groups (f76535e)
  • Made sure that the TSNE perplexity fits the sample size in plot_embeddings (d5f5d4e)
  • Fixed an edge case in which user-provided embeddings as DataFrames were misformatted in plot_embeddings (d5f5d4e)
  • Supported the case where no labels are provided to plot_embeddings (d5f5d4e)
  • Fixed a potential format mismatch in get_meta_analysis if random-effects meta-analyses were performed (d5f5d4e)
  • Fixed an issue where variance-filtered rows could cause problems in get_differential_expression if "monte_carlo = True" (ef3da9c)
  • Fixed an issue in get_differential_expression if "sets = True" that caused indexing issues under certain conditions (ef3da9c)
  • Ensured that "effect_size_variance = True" in get_differential_expression always formats variances correctly (ef3da9c)
  • Ensured that the combination of "grouped_BH = True", "paired = False", and CLR/ALR in get_differential_expression works even when negative values are present (87ea2fc)

regex

Changed 🔄
  • Improved tracing in try_matching for complicated branching cases (f394bda)
  • Ensured that format_retrieved_matches outputs the identified motifs in the canonical IUPAC representation (7558d9b)
Deprecated ⚠️
  • Deprecated process_pattern; will be done in-line instead (f394bda)
  • Deprecated expand_pattern; will be handled by specify_linkages and improvements in subgraph_isomorphism instead (f394bda)
  • Deprecated filter_dealbreakers; will be handled by improvements in subgraph_isomorphism instead (65bd12c)
Fixed 🐛
  • Fixed an issue in get_match_batch, in which precompiled patterns caused issues in get_match (194f31c)

annotate

Added ✨
  • Added get_size_branching_features to create glycan size and branching level features for downstream analysis (d57b836)
  • Added the "size_branch" option in the "feature_set" keyword argument of annotate_dataset and quantify_motifs, to analyze glycans by size or level of branching (d57b836)
Fixed 🐛
  • Fixed an issue in clean_up_heatmap in which, occasionally, duplicate strings were introduced in the output (e3eeb32)

ml

model_training

Added ✨
  • Added classification-AUROC, multilabel-accuracy, multilabel-MCC, regression-MAE, and regression-R2 as metrics to train_model (#66)
  • Added the "return_metrics" keyword argument to train_model that can additionally return all training and validation metrics (#66)
Changed 🔄
  • Weigh metric calculation by batch-size (correctly handling the last batch) in train_model (#66)
  • Best performances in train_model are now taken from the overall best model (lowest loss), not from best-model-per-metric (#66)
Fixed 🐛
  • Fixed an indexing issue in train_ml_model if "additional_features_train" / "additional_features_test" were used (b94744e)

inference

Changed 🔄
  • Changed resources.open_text to resources.files to prevent DeprecationWarning from importlib (d1a8c6d)

models

Changed 🔄
  • In prep_model, the hidden_dim argument can now also be used to modify the protein embedding size of a newly defined LectinOracle model (d1ff321)

network

evolution

Fixed 🐛
  • Fixed DeprecationWarning in distance_from_embeddings to prevent DataFrameGroupBy.apply from operating on the grouping columns (94646ad)
  • Fixed an issue in distance_from_metric where networks were indexed incorrectly based on presented DataFrame order (d2f5d55)

biosynthesis

Changed 🔄
  • Made sure in network_alignment that only nodes that are virtual in all aligned networks stay virtual (918d18f)
  • choose_leaves_to_extend will now correctly return no leaf node glycan if the target composition cannot be reached from any of the leaf nodes in a network (918d18f)
Fixed 🐛
  • Fixed an issue in find_shared_virtuals in which no shared nodes were found because of graph comparisons (d2f5d55)