Skip to content

Commit

Permalink
Update reactome dump
Browse files Browse the repository at this point in the history
  • Loading branch information
@ddomingof
ddomingof committed Mar 10, 2020
1 parent 4b1d113 commit 5a22fe2
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions src/pathme/constants.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def get_data_dir() -> str:
REACTOME = 'reactome'
REACTOME_DIR = os.path.join(DATA_DIR, REACTOME)
REACTOME_BEL = os.path.join(REACTOME_DIR, 'bel')
REACTOME_FILES = os.path.join(REACTOME_DIR, 'rdf')
REACTOME_FILES = os.path.join(REACTOME_DIR, 'rdf', 'biopax')

WIKIPATHWAYS = 'wikipathways'
WIKIPATHWAYS_DIR = os.path.join(DATA_DIR, WIKIPATHWAYS)
Expand Down Expand Up @@ -111,7 +111,7 @@ def ensure_pathme_folders():
WIKIPATHWAYS_REACTOME_MAPPINGS = 'https://github.com/ComPath/curation/raw/master/mappings/wikipathways_reactome.xlsx'

KEGG_KGML_URL = 'http://rest.kegg.jp/get/{}/kgml'
RDF_REACTOME = 'ftp://ftp.ebi.ac.uk/pub/databases/RDF/reactome/r67/reactome-biopax.tar.bz2'
RDF_REACTOME = 'ftp://ftp.ebi.ac.uk/pub/databases/RDF/reactome/r71/reactome-biopax.tar.bz2'
RDF_WIKIPATHWAYS = 'http://data.wikipathways.org/20190910/rdf/wikipathways-20190910-rdf-wp.zip'

KEGG_STATS_COLUMN_NAMES = {
Expand Down

1 comment on commit 5a22fe2

@cthoyt
Copy link
Member

@cthoyt cthoyt commented on 5a22fe2 Mar 10, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

maybe take this out of the URL constant and store the Reactome version as its own variable (then format it in). Same with wikipathways

Please sign in to comment.