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Dedicated library to query and retrieve data from Entrez databases at NCBI

Project description

# README

## Synopsis
`entrezpy` is a dedicated Python library to query and retrieve data from Entrez
databases at NCBI in analysis pipelines. It supports multi-threading, has no
external dependencies, and simplifies the construction of complex queries. Its
design allows to adjust for specific data types and formats without the need to
change the underlying functions.

## NCBI Website and Data Usage Policies and Disclaimers

https://www.ncbi.nlm.nih.gov/home/about/policies/

## Installation

### Cloning repository

Repository without wiki:

- `git clone https://gitlab.com/ncbipy/entrezpy.git`

Whole repository:

- `git >=2.13`:
- `git clone --recurse-submodules -j2 https://gitlab.com/ncbipy/entrezpy.git`

- `git >= 1.65`:
- `git clone --recursive https://gitlab.com/ncbipy/entrezpy.git`

- `git < 1.65`:

0. `git clone https://gitlab.com/ncbipy/entrezpy.git`
1. `cd ncbipy_eutils`
2. `git submodule update --init --recursive`

### Import
For example, import the esearch library add following lines to your code:
```
sys.path.insert(1, os.path.join(sys.path[0], 'path/to/entrezpy/src'))
import esearch.esearcher
import esearch.esearch_analyzer
```


### Create documentation

`entrezpy` is documented with `doxygen`(http://doxygen.nl/). To create the
documentation, `doxygen` has to be installed. The following command will create
the `entrzpy` LaTeX documentation at `doc/dox/latex/refman.pdf` and HTML
documentation at `doc/dox/html/index.html` ( `$REPOROOT` indicates the root
directory of the repository)

0. `cd $REPOROOT`
0. `doxygen entrezpy.dox`

### Examples

Ready to use examples using ncbipy-eutils are given in the repository
[https://gitlab.com/ncbipy/entrezpy.git].


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