v1.2.0

Change Log

For Version 1.2.0

• Added glycoworkGUI.py to build the .exe based GUI for important glycowork endpoint functions: GlycoDraw, plot_glycans_excel, and get_differential_expression
• Removed python-louvain as a required dependency for glycowork

glycan_data

loader

• Switched from pkg_resources to importlib for loading tabular data into the package
  stats
• Fixed an issue in TST_grouped_benjamini_hochberg that caused errors if nothing was significantly different in the entire dataset or in any group
• test_inter_vs_intra_grouping is now robust to non-paired data and data with differing sample sizes per condition
• Added replace_outliers_with_IQR_bounds to support outlier treatment in motif.analysis
• Added sequence_richness, shannon_diversity_index, and simpson_diversity_index to calculate diversity indices of glycomics data

motif

processing

• WURCS handling for universal input now encompass more monosaccharides
• GlycoCT handling for universal input now is robust to the declaration of substituents not immediately following their monosaccharide in the GlycoCT string
• Added equal_repeats to check whether two repeating units of a polysaccharide are the same, just shifted
• Modified glycan nomenclature detection in canonicalize_iupac to be less prone of overidentifying Oxford when it’s just numbers etc.
• Added “ß” to the typo detection in canonicalize_iupac and “(-)” as a variation of linkage uncertainty detection
• Made canonicalize_iupac robust to the variation of using {} instead of () for linkages

graph

• Removed the required usage of lib in glycan_to_nxGraph, compare_glycans, subgraph_isomorphism, and all downstream functions (lib only remains for stemification and deep learning model training/inference)
• The keyword argument “wildcards_ptm” now also works as intended when providing pre-calculated graphs as input to compare_glycans or subgraph_isomorphism
• Fixed a rare issue in which subgraph_isomorphism, when “count = False”, would sometimes erroneously output “False” because of a greedy approach to evaluating potential matches

tokenization

• Added get_unique_topologies to retrieve all base topologies for a given composition that have been observed for a given taxonomic subset
• Added the “obfuscate_ptm” keyword argument to map_to_basic, to allow for mapping Gal6S to Hex6S rather than the default HexOS, if that is required/advantageous
• Support mapping of phosphorylated glycans in map_to_basic

draw

• Fixed an issue where cross-ring fragments were not correctly rendered in GlycoDraw
• plot_glycans_excel can now also be used with filepaths to .xlsx files (in addition to .csv files)
• plot_glycans_excel now also supports compact glycan drawing with the “compact” keyword argument
• Improved drawing resolution in plot_glycans_excel
• GlycoDraw will now more strongly make use of nomenclature canonicalization in case of IUPAC dialects (still not 100%, if you suspect you use a dialect of IUPAC, pass your sequences through canonicalize_iupac first)
• If no filepath is specified, GlycoDraw will now also display drawn glycan structures in a non-Jupyter environment (as the classic matplotlib pop-up). Note that this functionality requires the cairosvg dependency (head to https://bojarlab.github.io/glycowork/examples.html#glycodraw-code-snippets if you’re unsure about that)

analysis

• Functions able to use .csv paths as input can now also deal with .xlsx paths as input
• The new “annotate_volcano” keyword argument now allows for the direct insertion of SNFG images within plots from get_volcano without having to subsequently run draw.annotate_figure
• get_pvals_motifs, get_differential_expression, get_glycanova, get_time_series, and get_jtk now use glycan_data.stats.replace_outliers_with_IQR_bounds to auto-smooth outliers
• Moved hotellings_t2 to glycan_data.stats
• All functions compatible with motif-level analysis now accept the “custom_motifs” keyword argument to be passed to annotate_dataset or quantify_motifs if “custom” is included in “feature_set”
• Changed the “mode” keyword argument in get_heatmap to “motifs” as a Boolean argument, like in all other motif.analysis functions
• Added a call to clean_up_heatmap to get_jtk to avoid redundant motifs
• Added get_biodiversity to compare two groups of glycomics datasets with regard to the sequence diversity that is present (similar to comparable analyses for microbiome data)

regex

• Added filter_dealbreakers to allow for the exclusion of identified matches if they have illegal components beyond the identified match (e.g., the forbidden Fuc in "Fuc-([Gal|GalNAc])?-Gal-([!Fuc]){,1}-GlcNAc"). Before this, the sequence context except the Fuc was extracted and returned.
• Fixed an edge case in filter_matches_by_location in which internal locations sometimes had to handle triple-nested lists which led to errors
• get_match can now also use glycan graphs, such as derived from glycan_to_nxGraph, as input
• Added get_match_batch to process a whole list of glycans at once, with some performance improvements via first pre-compiling the pattern
• Fixed an edge case in get_match in which pattern components consisting of a single monosaccharide with a specified linkage (e.g., “Fuca3”) could sometimes erroneously output no matches
• Added motif_to_regex to convert glycan motifs (e.g., in IUPAC-condensed) into a regular expression suitable for get_match. Limited to simple queries for now.

annotate

• get_terminal_structures now has a “size” keyword argument with which users can control the size of the extracted terminal motifs
• get_k_saccharides now has a “terminal” keyword argument with which users can filter to only count motifs at non-reducing ends
• annotate_dataset and functions using it now can add the “terminal2” and “terminal3” option in “feature_set” to also annotate & analyze terminal motifs of size 2 (e.g., Neu5Ac(a2-3)Gal(b1-4)) or size 3 (e.g., Neu5Ac(a2-3)Gal(b1-4)GlcNAc)

network

biosynthesis

• Added the possibility of providing abundances to construct_network that are then stored as node attributes in the network
• Added add_high_man_removal as a post-processing step in construct_network to allow for the addition of reactions removing mannoses from high-Man N-glycans occurring during maturation
• Added estimate_weights and get_edge_weight_by_abundance to estimate reaction capacities from abundances + estimate missing abundances
• Added get_maximum_flow, get_max_flow_path, and get_reaction_flow to calculate maximum flow paths between network root and endpoints as well as aggregate the flow by reaction type
• Added get_differential_biosynthesis as a wrapper function to compare two groups of glycomes/networks with regard to their biosynthesis (differential flow paths or differential reaction flows)
• Fixed an issue in construct_network in which sometimes nodes with outgoing but no incoming connections were not detected as unconnected nodes, leading to incomplete networks
• Added the rescue_glycans decorator to construct_network, to allow for auto-fixing nomenclature variations
• Improved performance of construct_network by reducing wasteful computation

evolution

• Switched get_communities from using python-louvain to the Louvain implementation in networkx