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stop modifying dicts in place in composition_to_mass
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@Bribak
Bribak committed Nov 7, 2024
1 parent 27ae4df commit a6905dc
Showing 1 changed file with 26 additions and 47 deletions.
73 changes: 26 additions & 47 deletions glycowork/motif/tokenization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,7 @@ def constrain_prot(proteins, libr = None):
| libr (list): sorted list of amino acids occurring in proteins\n
| Returns:
| :-
| Returns list of proteins with only permitted amino acids
"""
| Returns list of proteins with only permitted amino acids"""
if libr is None:
libr = chars
# Check whether any character is not in libr and replace it with a 'z' placeholder character
Expand All @@ -46,8 +45,7 @@ def prot_to_coded(proteins, libr = None, pad_len = 1000):
| pad_len (int): length up to which the proteins are padded\n
| Returns:
| :-
| Returns list of encoded proteins with only permitted amino acids
"""
| Returns list of encoded proteins with only permitted amino acids"""
if libr is None:
libr = chars
pad_label = len(libr) - 1
Expand All @@ -69,8 +67,7 @@ def string_to_labels(character_string, libr = None):
| libr (dict): dict of library items\n
| Returns:
| :-
| Returns indexes of characters in library
"""
| Returns indexes of characters in library"""
if libr is None:
libr = chars
return list(map(libr.get, character_string))
Expand All @@ -83,11 +80,10 @@ def pad_sequence(seq, max_length, pad_label = None, libr = None):
| seq (list): sequence to pad (from string_to_labels)
| max_length (int): sequence length to pad to
| pad_label (int): which padding label to use
| libr (list): list of library items\n\n
| libr (list): list of library items\n
| Returns:
| :-
| Returns padded sequence
"""
| Returns padded sequence"""
if libr is None:
libr = chars
if pad_label is None:
Expand All @@ -105,8 +101,7 @@ def get_core(sugar):
| sugar (string): monosaccharide or linkage\n
| Returns:
| :-
| Returns core monosaccharide as string
"""
| Returns core monosaccharide as string"""
easy_cores = set(['dHexNAc', 'GlcNAc', 'GalNAc', 'ManNAc', 'FucNAc', 'QuiNAc', 'RhaNAc', 'GulNAc',
'IdoNAc', 'Ins', 'MurNAc', '6dAltNAc', 'AcoNAc', 'HexA', 'GlcA', 'AltA',
'GalA', 'ManA', 'Tyv', 'Yer', 'Abe', 'GlcfNAc', 'GalfNAc', 'ManfNAc',
Expand Down Expand Up @@ -144,8 +139,7 @@ def get_modification(sugar):
| sugar (string): monosaccharide or linkage\n
| Returns:
| :-
| Returns modification as string
"""
| Returns modification as string"""
core = get_core(sugar)
modification = sugar.replace(core, '')
return modification
Expand All @@ -158,8 +152,7 @@ def get_stem_lib(libr):
| libr (dict): dictionary of form glycoletter:index\n
| Returns:
| :-
| Returns dictionary of form modified_monosaccharide:core_monosaccharide
"""
| Returns dictionary of form modified_monosaccharide:core_monosaccharide"""
return {k: get_core(k) for k in libr}


Expand All @@ -175,8 +168,7 @@ def stemify_glycan(glycan, stem_lib = None, libr = None):
| libr (dict): dictionary of form glycoletter:index; default:lib\n
| Returns:
| :-
| Returns stemmed glycan as string
"""
| Returns stemmed glycan as string"""
if libr is None:
libr = lib
if stem_lib is None:
Expand Down Expand Up @@ -236,8 +228,7 @@ def stemify_dataset(df, stem_lib = None, libr = None,
| rarity_filter (int): how often monosaccharide modification has to occur to not get removed; default:1\n
| Returns:
| :-
| Returns df with glycans stemified
"""
| Returns df with glycans stemified"""
if libr is None:
libr = lib
if stem_lib is None:
Expand Down Expand Up @@ -272,8 +263,7 @@ def mz_to_composition(mz_value, mode = 'negative', mass_value = 'monoisotopic',
| adduct (string): chemical formula of adduct that contributes to m/z, e.g., "C2H4O2"; default:None\n
| Returns:
| :-
| Returns a list of matching compositions in dict form
"""
| Returns a list of matching compositions in dict form"""
if df_use is None:
if glycan_class == "all":
df_use = df_glycan[df_glycan.Kingdom.apply(lambda x: kingdom in x)]
Expand Down Expand Up @@ -324,8 +314,7 @@ def match_composition_relaxed(composition, glycan_class = 'N', kingdom = 'Animal
| df_use (dataframe): glycan dataframe for searching glycan structures; default:df_glycan\n
| Returns:
| :-
| Returns list of glycans matching composition in IUPAC-condensed
"""
| Returns list of glycans matching composition in IUPAC-condensed"""
if df_use is None:
df_use = df_glycan[(df_glycan.glycan_type == glycan_class) & (df_glycan.Kingdom.apply(lambda x: kingdom in x))]
# Subset for glycans with the right number of monosaccharides
Expand All @@ -344,8 +333,7 @@ def condense_composition_matching(matched_composition):
| matched_composition (list): list of glycans matching to a composition\n
| Returns:
| :-
| Returns minimal list of glycans that match a composition
"""
| Returns minimal list of glycans that match a composition"""
# Establish glycan equality given the wildcards
match_matrix = pd.DataFrame(
[[compare_glycans(k, j)
Expand Down Expand Up @@ -382,8 +370,7 @@ def compositions_to_structures(composition_list, glycan_class = 'N', kingdom = '
| verbose (bool): whether to print any non-matching compositions; default:False\n
| Returns:
| :-
| Returns dataframe of (matched structures) x (relative intensities)
"""
| Returns dataframe of (matched structures) x (relative intensities)"""
if df_use is None:
df_use = df_glycan[(df_glycan.glycan_type == glycan_class) & (df_glycan.Kingdom.apply(lambda x: kingdom in x))]
if abundances is None:
Expand Down Expand Up @@ -433,8 +420,7 @@ def mz_to_structures(mz_list, glycan_class, kingdom = 'Animalia', abundances = N
| verbose (bool): whether to print any non-matching compositions; default:False\n
| Returns:
| :-
| Returns dataframe of (matched structures) x (relative intensities)
"""
| Returns dataframe of (matched structures) x (relative intensities)"""
if df_use is None:
df_use = df_glycan[(df_glycan.glycan_type == glycan_class) & (df_glycan.Kingdom.apply(lambda x: kingdom in x))]
if filter_out is None:
Expand Down Expand Up @@ -468,8 +454,7 @@ def mask_rare_glycoletters(glycans, thresh_monosaccharides = None, thresh_linkag
| thresh_linkages (int): threshold-value for linkages seen as "rare"; default:(0.03*len(glycans))\n
| Returns:
| :-
| Returns list of glycans in IUPAC-condensed with masked rare monosaccharides and linkages
"""
| Returns list of glycans in IUPAC-condensed with masked rare monosaccharides and linkages"""
# Get rarity thresholds
if thresh_monosaccharides is None:
thresh_monosaccharides = int(np.ceil(0.001*len(glycans)))
Expand Down Expand Up @@ -512,8 +497,7 @@ def map_to_basic(glycoletter, obfuscate_ptm = True):
| obfuscate_ptm (bool): whether to remove position-specific information of PTM or not; default:True\n
| Returns:
| :-
| Returns the base monosaccharide/linkage or the original glycoletter, if it cannot be mapped
"""
| Returns the base monosaccharide/linkage or the original glycoletter, if it cannot be mapped"""
conditions = [(Hex, 'Hex'), (dHex, 'dHex'), (HexA, 'HexA'), (HexN, 'HexN'), (HexNAc, 'HexNAc'), (Pen, 'Pen'), (linkages, '?1-?')]
for cond, ret in conditions:
if glycoletter in cond:
Expand Down Expand Up @@ -543,8 +527,7 @@ def structure_to_basic(glycan):
| glycan (string): glycan in IUPAC-condensed nomenclature\n
| Returns:
| :-
| Returns the glycan topology as a string
"""
| Returns the glycan topology as a string"""
if glycan.endswith('-ol'):
glycan = glycan[:-3]
if '(' not in glycan:
Expand All @@ -564,8 +547,7 @@ def glycan_to_composition(glycan, stem_libr = None):
| stem_libr (dictionary): dictionary of form modified_monosaccharide:core_monosaccharide; default:created from lib\n
| Returns:
| :-
| Returns a dictionary of form "Monosaccharide" : count
"""
| Returns a dictionary of form "Monosaccharide" : count"""
if stem_libr is None:
stem_libr = stem_lib
if '{' in glycan:
Expand Down Expand Up @@ -596,8 +578,7 @@ def calculate_adduct_mass(adduct, mass_value = 'monoisotopic'):
| mass_value (string): whether to use 'monoisotopic' or 'average' mass; default:'monoisotopic'\n
| Returns:
| :-
| Returns the mass of the adduct
"""
| Returns the mass of the adduct"""
element_masses = {
'monoisotopic': {'C': 12.0000, 'H': 1.0078, 'O': 15.9949, 'N': 14.0031},
'average': {'C': 12.0107, 'H': 1.00794, 'O': 15.9994, 'N': 14.0067}
Expand All @@ -622,18 +603,18 @@ def calculate_adduct_mass(adduct, mass_value = 'monoisotopic'):


@rescue_compositions
def composition_to_mass(dict_comp, mass_value = 'monoisotopic', sample_prep = 'underivatized', adduct = None):
def composition_to_mass(dict_comp_in, mass_value = 'monoisotopic', sample_prep = 'underivatized', adduct = None):
"""given a composition, calculates its theoretical mass; only allowed extra-modifications are methylation, sulfation, phosphorylation\n
| Arguments:
| :-
| dict_comp (dict): composition in form monosaccharide:count
| dict_comp_in (dict): composition in form monosaccharide:count
| mass_value (string): whether the expected mass is 'monoisotopic' or 'average'; default:'monoisotopic'
| sample_prep (string): whether the glycans has been 'underivatized', 'permethylated', or 'peracetylated'; default:'underivatized'
| adduct (string): chemical formula of adduct to be added, e.g., "C2H4O2"; default:None\n
| Returns:
| :-
| Returns the theoretical mass of input composition
"""
| Returns the theoretical mass of input composition"""
dict_comp = dict_comp_in.copy()
mass_key = f"{sample_prep}_{mass_value}"
mass_dict_in = mass_dict if mass_key == "underivatized_monoisotopic" else dict(zip(mapping_file.composition, mapping_file[mass_key]))
for old_key, new_key in {'S': 'Sulphate', 'P': 'Phosphate', 'Me': 'Methyl', 'Ac': 'Acetate'}.items():
Expand All @@ -657,8 +638,7 @@ def glycan_to_mass(glycan, mass_value = 'monoisotopic', sample_prep = 'underivat
| adduct (string): chemical formula of adduct to be added, e.g., "C2H4O2"; default:None\n
| Returns:
| :-
| Returns the theoretical mass of input glycan
"""
| Returns the theoretical mass of input glycan"""
if stem_libr is None:
stem_libr = stem_lib
comp = glycan_to_composition(glycan, stem_libr = stem_libr)
Expand All @@ -679,8 +659,7 @@ def get_unique_topologies(composition, glycan_type, df_use = None, universal_rep
| taxonomy_value (string): which value to filter at taxonomy_rank; default: Animalia\n
| Returns:
| :-
| Returns a list of observed base topologies for the given composition
"""
| Returns a list of observed base topologies for the given composition"""
if df_use is None:
df_use = df_glycan
if universal_replacers is None:
Expand Down

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