diff options
Diffstat (limited to 'backend/tolData/genOtolData.py')
| -rwxr-xr-x | backend/tolData/genOtolData.py | 27 |
1 files changed, 12 insertions, 15 deletions
diff --git a/backend/tolData/genOtolData.py b/backend/tolData/genOtolData.py index 4236999..6310cc9 100755 --- a/backend/tolData/genOtolData.py +++ b/backend/tolData/genOtolData.py @@ -3,31 +3,28 @@ import sys, re, os import json, sqlite3 -usageInfo = f""" -Usage: {sys.argv[0]} - +import argparse +parser = argparse.ArgumentParser(description=""" Reads files describing a tree-of-life from an 'Open Tree of Life' release, and stores tree info in a database. Reads a labelled_supertree_ottnames.tre file, which is assumed to have this format: The tree-of-life is represented in Newick format, which looks like: (n1,n2,(n3,n4)n5)n6 - The root node is named n6, and has children n1, n2, and n5. + The root node is named n6, and has children n1, n2, and n5. Name examples include: Homo_sapiens_ott770315, mrcaott6ott22687, 'Oxalis san-miguelii ott5748753', - 'ott770315' and 'mrcaott6ott22687' are node IDs. The latter is for a 'compound node'. - The node with ID 'ott770315' will get the name 'homo sapiens'. - A compound node will get a name composed from it's sub-nodes (eg: [name1 + name2]). - It is possible for multiple nodes to have the same name. - In these cases, extra nodes will be named sequentially, as 'name1 [2]', 'name1 [3]', etc. + 'ott770315' and 'mrcaott6ott22687' are node IDs. The latter is for a 'compound node'. + The node with ID 'ott770315' will get the name 'homo sapiens'. + A compound node will get a name composed from it's sub-nodes (eg: [name1 + name2]). + It is possible for multiple nodes to have the same name. + In these cases, extra nodes will be named sequentially, as 'name1 [2]', 'name1 [3]', etc. Reads an annotations.json file, which is assumed to have this format: Holds a JSON object, whose 'nodes' property maps node IDs to objects holding information about that node, such as the properties 'supported_by' and 'conflicts_with', which list phylogenetic trees that - support/conflict with the node's placement. + support/conflict with the node's placement. Reads from a picked-names file, if present, which specifies name and node ID pairs. - These help resolve cases where multiple nodes share the same name. -""" -if len(sys.argv) > 1: - print(usageInfo, file=sys.stderr) - sys.exit(1) + These help resolve cases where multiple nodes share the same name. +""", formatter_class=argparse.RawDescriptionHelpFormatter) +parser.parse_args() treeFile = "otol/labelled_supertree_ottnames.tre" # Had about 2.5e9 nodes annFile = "otol/annotations.json" |