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

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

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

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

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

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)

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)

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.

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)

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

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