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Formater --mesh

A simple code to get link betweenn MESH Term.

Requirements

Quick start

# Clone the project
$ git clone https://github.com/thomasdenecker/IronYeasts.git
$ cd IronYeasts
# Install pipenv
$ pipenv install --ignore-pipfile
# Have help
python3 formater.py --help
# Run mesh_link with exemple files
$ pipenv run python formater.py --mesh -i tests/MESH/MESH_input_test.bin -o ./Outputs/demo_MESH

Usage

$ python formater.py --help
usage: formater.py [-h] [-i INPUT] [-o OUTPUT] [--mesh] [--go] [--gryc]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        For MESH, a Mesh file (bin format find here
                        (dYEAR.bin, ie. d2018.bin):
                        ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/
                        asciimesh/). For GO, a GO terms file (obo format find
                        here : (go.obo, ie. go.obo :
                        http://purl.obolibrary.org/obo/go.obo). By default,
                        the last version.For GRYC a folder with EMBL files
  -o OUTPUT, --output OUTPUT
                        Output file name (whithout format (.txt))
  --mesh                Converte raw mesh file to link table
  --go                  Associate GO term and its definition
  --gryc                Generate table with all annotations of GRYC

MESH

The MESH or Medical Subject Headings is the thesaurus of the National Library of Medicine's controlled vocabulary. It consists of sets of terms naming descriptors in a hierarchical structure allowing search at different levels of specificity (https://meshb.nlm.nih.gov/search). It is possible to download all the MESHs. An important point of the MESH term is that other MESH terms are recommended for reading. This code generate a link table between a MESH term and MESH terms associated.