diff options
Diffstat (limited to 'backend/data/genOtolData.py')
| -rwxr-xr-x | backend/data/genOtolData.py | 16 |
1 files changed, 8 insertions, 8 deletions
diff --git a/backend/data/genOtolData.py b/backend/data/genOtolData.py index 7dfac54..9298106 100755 --- a/backend/data/genOtolData.py +++ b/backend/data/genOtolData.py @@ -1,12 +1,12 @@ #!/usr/bin/python3 -import sys, re, json, sqlite3 -import os.path +import sys, os.path, re +import json, sqlite3 usageInfo = f"usage: {sys.argv[0]}\n" -usageInfo += "Reads labelled_supertree_ottnames.tre & annotations.json (from an Open Tree of Life release), \n" +usageInfo += "Reads labelled_supertree_ottnames.tre & annotations.json (from an Open Tree of Life release),\n" usageInfo += "and creates a sqlite database, which holds entries of the form (name text, data text).\n" -usageInfo += "Each row holds a tree-of-life node's name, JSON-encoded child name array, a parent name or '', \n" +usageInfo += "Each row holds a tree-of-life node's name, JSON-encoded child name array, a parent name or '',\n" usageInfo += "number of descendant 'tips', and a 1 or 0 indicating phylogenetic-support.\n" usageInfo += "\n" usageInfo += "Expected labelled_supertree_ottnames.tre format:\n" @@ -30,10 +30,10 @@ idToName = {} # Maps node IDs to names nameToFirstId = {} # Maps node names to first found ID (names might have multiple IDs) dupNameToIds = {} # Maps names of nodes with multiple IDs to those node IDs -## Check for existing db -#if os.path.exists(dbFile): -# print("ERROR: Existing {} db".format(dbFile), file=sys.stderr) -# sys.exit(1) +# Check for existing db +if os.path.exists(dbFile): + print("ERROR: Existing {} db".format(dbFile), file=sys.stderr) + sys.exit(1) # Parse treeFile print("Parsing tree file") data = None |