https://github.com/nalomran/pubmed2doc
Write PubMed search results with two display options (citation or listview) to PDF or Word
https://github.com/nalomran/pubmed2doc
bioinformatics biopython docx fpdf pubmed pubmed-parser python3
Last synced: 6 months ago
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Write PubMed search results with two display options (citation or listview) to PDF or Word
- Host: GitHub
- URL: https://github.com/nalomran/pubmed2doc
- Owner: nalomran
- License: mit
- Created: 2020-09-22T09:26:16.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-10-18T19:31:27.000Z (about 5 years ago)
- Last Synced: 2025-03-25T04:06:19.206Z (7 months ago)
- Topics: bioinformatics, biopython, docx, fpdf, pubmed, pubmed-parser, python3
- Language: Python
- Homepage:
- Size: 269 KB
- Stars: 13
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# pubmed2doc
## Introduction
Would you like your PubMed search results to be saved as PDF or Ms Word file format? If yes, then look
no further, I present to you **pubmed2doc**, a python module implemented to write your PubMed search
results to PDF or Word file. The basic workflow of the module in a nutshell is as follow:
1. It takes your query as an input and searches it against the PubMed database.
2. The returned PubMed results will be then prepared in one of the two display options i.e citation or listview (based
on the user's choice).
3. The prepared results will finally be written to user's supplied file choice (PDF or Word).
To my knowledge, PubMed doesn't offer this feature i.e saving (or exporting) the search results to PDF or Word and
therefore this module provides the following advantages:
1. It doesn't require any intermediate software to aid in exporting the PubMed results to PDF or Word.
2. It Keeps the document stored locally and can be retrieved at a later time.
2. The generated document is easier to read, view and edit comparing with the csv or text files exported by PubMed.
3. It can also be ported or incorporated easily into the user's own research resources.
## Getting Started
* You need to have python version >= 3.4 installed and a terminal (or similar program) to execute
the module through the command line.
* The following sections will guide you to execute the module successfully in a step-by-step fashioned.
## Prerequisites
* The following are the core Python libraries (dependencies) required for this module:
```bash
biopython
fpdf
python-docx
```
## Install
1. First, you need to download the compressed file in GitHub.
2. Uncompress it and change to the directory ```cd```:
```bash
unzip Pubmed_To_Docs.zip
cd Pubmed_To_Docs/
```
3. It is highly recommended to create conda or python virtual environment and
install the aforementioned dependencies within such environment (OPTIONAL):
* Creating conda virtual environment, please change "your_env_name" your desire environment name:
```bash
conda create -n your_env_name
conda activate your_env_name
```
* Creating python virtual environment:
```bash
pip install virtualenv
virtualenv your_env_name
source your_env_name/bin/activate
```
* **Note:** don't forget to de-activate your environment once you are completely done running the module:
```bash
# for conda env
conda deactivate
# for python env
deactivate
```
4. You may now try to install the dependencies by running the following command:
```bash
sudo pip install -r requirements.txt
```
- You will be prompted to enter a password if you run the ```sudo``` command, the password is
the root password (system administrator) of the computer you are currently running.
## Running the Module (pubmed2doc.py)
* Please make sure you are in the same directory location as the module pubmed2doc.py, and you may try to
check the presence of the module by running the following command:
```bash
ls -ltrh *.py
* #### Inputs + Options
+ -q: a query to be searched against PubMed database (REQUIRED)
+ -e: a user's email to access to the PubMed db (REQUIRED)
+ -pdf: write PubMed results to PDF (OPTIONAL) (Default value is True)
+ -word: write PubMed results to Word (OPTIONAL) (Default value is False)
+ -retmax: total num of records from query to be retrieved (OPTIONAL)
(Default value is 20)
+ -sopt: type of returned results display options (citation or listview)
(OPTIONAL) (Default is citation)
+ -mndate: custom start or minimum publication date (OPTIONAL)"
+ -mxdate: custom end or maximum publication date (OPTIONAL)"
+ is_abstract: include abstract to your search results
* #### List All Module Parameters
- You can list all the module parameters by running the following command:
```bash
python pubmed2doc.py -h
```
* #### Output
+ A Word or PDF document consists of the results from PubMed according to the type of display option
chosen by the user
### 1. Executing it with python command:
* #### Command Example
```bash
python pubmed2doc.py \
-q "gene expression" \
-e "your_email" \
-pdf F \
-word T \
-sopt listview
```
* The above command is just an example, you can create your own advance query and include other arguments, please see
above sub-section "Inputs + Options"
* Please note that the output file will be saved in a directory called "output"
### 2. Executing it with the prepared shell script:
* #### Command Example
```bash
example_command.sh
```
* You can modify the shell script to follow your needs.
* That is it! Please check the output folder for your file
## Asking for Help
If you have an issue (error or bug) when executing the module or have any other enquires please feel free to send
me an [email](mailto:nawafalomran@hotmail.com) and I will reply as soon as I can