WBtools
Interface to WormBase curation database and Text Mining functions
Access WormBase paper corpus information by loading pdf files (converted to txt) and curation info from the WormBase database. The package also exposes text mining functions on papers' fulltext.
Installation
pip install wbtools
Usage example
Get sentences from a WormBase paper
from wbtools.literature.corpus import CorpusManager
paper_id = "00050564"
cm = CorpusManager()
cm.load_from_wb_database(db_name="wb_dbname", db_user="wb_dbuser", db_password="wb_dbpasswd", db_host="wb_dbhost",
paper_ids=[paper_id], file_server_host="file_server_base_url", file_server_user="username",
file_server_passwd="password")
sentences = cm.get_paper(paper_id).get_text_docs(split_sentences=True)
Get the latest papers (up to 50) added to WormBase or modified in the last 30 days
from wbtools.literature.corpus import CorpusManager
import datetime
one_month_ago = (datetime.datetime.now() - datetime.timedelta(days=30)).strftime("%M/%D/%Y")
cm = CorpusManager()
cm.load_from_wb_database(db_name="wb_dbname", db_user="wb_dbuser", db_password="wb_dbpasswd", db_host="wb_dbhost",
from_date=one_month_ago, max_num_papers=50,
file_server_host="file_server_base_url", file_server_user="username",
file_server_passwd="password")
paper_ids = [paper.paper_id for paper in cm.get_all_papers()]
Get the latest 50 papers added to WormBase or modified that have a final pdf version and have been flagged by WB paper classification pipeline, excluding reviews and papers with temp files only (proofs)
from wbtools.literature.corpus import CorpusManager
import datetime
cm = CorpusManager()
cm.load_from_wb_database(db_name="wb_dbname", db_user="wb_dbuser", db_password="wb_dbpasswd", db_host="wb_dbhost",
max_num_papers=50, must_be_autclass_flagged=True, exclude_pap_types=['Review'],
exclude_temp_pdf=True, file_server_host="file_server_base_url",
file_server_user="username", file_server_passwd="password")
paper_ids = [paper.paper_id for paper in cm.get_all_papers()]
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Release files for wbtools 3.5.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| wbtools-3.5.0.tar.gz | 39.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| wbtools-3.5.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 87.4 kB
Release files / wbtools-3.5.0.tar.gz
| Download URL | wbtools-3.5.0.tar.gz |
|---|---|
| Size | 39.6 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
Release files / wbtools-3.5.0-py3-none-any.whl
| Download URL | wbtools-3.5.0-py3-none-any.whl |
|---|---|
| Size | 47.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
