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modified: glycan_processing_helpers.py #2

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modified: glycan_processing_helpers.py #2

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19 changes: 10 additions & 9 deletions glycan_processing_helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,16 @@
import re

# Glycans by taxonomic levels
df_species = pd.read_csv('pydata/glyco_targets_species_seq_all_V2clean.csv')
df_species.domain = [k.strip() for k in df_species.domain.values.tolist()]
df_species.kingdom = [k.strip() for k in df_species.kingdom.values.tolist()]
df_species.phylum = [k.strip() for k in df_species.phylum.values.tolist()]
df_species['class'] = [k.strip() for k in df_species['class'].values.tolist()]
df_species.order = [k.strip() for k in df_species.order.values.tolist()]
df_species.family = [k.strip() for k in df_species.family.values.tolist()]
df_species.genus = [k.strip() for k in df_species.genus.values.tolist()]
df_species.target = [str(k) for k in df_species.target.values.tolist()]
#df_species = pd.read_csv('pydata/glyco_targets_species_seq_all_V2clean.csv')
#df_species.domain = [k.strip() for k in df_species.domain.values.tolist()]
#df_species.kingdom = [k.strip() for k in df_species.kingdom.values.tolist()]
#df_species.phylum = [k.strip() for k in df_species.phylum.values.tolist()]
#df_species['class'] = [k.strip() for k in df_species['class'].values.tolist()]
#df_species.order = [k.strip() for k in df_species.order.values.tolist()]
#df_species.family = [k.strip() for k in df_species.family.values.tolist()]
#df_species.genus = [k.strip() for k in df_species.genus.values.tolist()]
#df_species.target = [str(k) for k in df_species.target.values.tolist()]
df_species = pd.read_csv('pydata/v2_glycobase.csv')

# Lists of possible bonds and sugars
with open('pydata/all_bonds.pkl','rb') as file:
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