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utils for eutils (based on BioPython)

Python 31.74% Jupyter Notebook 68.26%

eutilsutils's Introduction

eutilsutils

Utilities for Entrez E-Utilities based on BioPython.

Notebooks

Some explanation of how to run BioPython and some of the code written in this repo will be demonstrated in Jupyter Notebooks which can be viewed here.

Scripts

The scripts directory will have some general utility scripts for testing the code or to demonstrate the functionality.

Installation and Running

Before first use:

Download and install Conda (Anaconda or Miniconda).
Clone this repo
Create a conda environment with the required dependencies.

$ conda create --name eutilsutils --file config/eutilsutils.yml

Before running the scripts:

Make sure you activate the conda environment

$ conda activate eutilsutils

eutilsutils's People

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eutilsutils's Issues

[S001] super user creates a blank DB

Schema Version 0.1 can be created via a script (not flask)

eFetch demo in BioEntrezGeneral.ipynb

Demo 3 techniques

Parse XML piecemeal using Entrez.parse()
Parse XML entirely using Entrez.read()
Parse MEDLINE stream piecemeal using Medline.parse()

Support granular table selection in makedb.py

Passed as values for the -t or --table argument

eSummary demo in BioEntrezGeneral.ipynb

eSearch demo in BioEntrezGeneral.ipynb

new script: pmid file --> csv output

scripts/pmid2csv.py

Simple script that reads a pmid file and generates a csv file.

Requires 2 arguments: input pmid file name, output csv file name

Initial operation description:

Use epost
Call non-paginated esummary (try to break in testing)
Fail if output file exists

Define esummary paper model

PMID
AUTHORS_DISP
TITLE
Source
SO

Read and store pmcid when importing eSummary

Add to pmid2psql.py

[S003] Browser home page shows count of publications in DB

Flask app

ePost demo in BioEntrezGeneral.ipynb

Flask app deployed using app factory

Move from global variable to app factory

Create reusable script output formatting and parsing

Similar to eutilsconfig.py but for script output utilities. For example the makeRed() and makeYellow() functions for tty; also parseargs.

[S002] Manually add pubmed records into PSQL db

DB Schema (defined) can be updated manually by user

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