Parsing the MeSH ASCII format in Python

Similar to our previously published UniProt parser, MeSH provides an ASCII format that can easily be parsed using Python.

Just like the UniProt parser, this function yields MeSH entries represented by dictionaries. Example code is included at the bottom of the file.

ParseMeSH.py download
#!/usr/bin/env python3
"""
A simple parse for the MeSH ASCII format, as downloadable from here:
on ftp://nlmpubs.nlm.nih.gov/online/mesh/.asciimesh/d2015.bin

For a reference on MeSH headings (i.e. keys in the resulting map), see
http://www.nlm.nih.gov/mesh/elmesh99.pdf

Originally published on TechOverflow.net
"""
from collections import defaultdict

__author__ = "Uli Koehler"
__copyright__ = "Copyright 2015, Uli Koehler"
__license__ = "Apache License v2.0"
__version__ = "1.0"


def readMeSH(fin):
    """
    Given a file-like object, generates MeSH objects, i.e.
    dictionaries with a list of values for each qualifier.

    Example: {"MH": ["Acetylcysteine"]}

    """
    currentEntry = None
    for line in fin:
        line = line.strip()
        if not line:
            continue
        # Handle new record. MeSH explicitly marks this
        if line == "*NEWRECORD":
            # Yiel old entry, initialize new one
            if currentEntry:
                yield currentEntry
            currentEntry = defaultdict(list)
            continue
        # Line example: "MH = Acetylcysteine"
        key, _, value = line.partition(" = ")
        # Append to value list
        currentEntry[key].append(value)
    # If there is a non-empty entry left, yield it
    if currentEntry:
        yield currentEntry

if __name__ == "__main__":
    # Example of how to use readMeSH()
    import argparse
    parser = argparse.ArgumentParser()
    parser.add_argument("file")
    args = parser.parse_args()
    with open(args.file, "r") as infile:
        # readMeSH() yields MeSH objects, i.e. dictionaries
        for entry in readMeSH(infile):
            print(entry)