fam-parser

FAM file parser

A library for parsing FAM files from Python or Javascript.

Python library

Installation:

pip install fam-parser

Use as a library:

import sys
from fam_parser import FamParser

parser = FamParser()
parser.read(open(example.fam'))
parser.write(sys.stdout)

Command line invocation:

fam_parser example.fam -

You can also invoke it directly from the repository root directory without installation:

python -m python.fam_parser example.fam -

Javascript library

Installation:

npm install fam-parser

Installation from source:

npm install
npm run dist

Use as a library:

var FamParser = require('fam-parser');

var parser = new FamParser(fs.readFileSync(
  'example.fam').toString('binary')
);

parser.getMembers().forEach(function(member) {
  console.log(member.SURNAME);
});

Command line invocation:

./node_modules/.bin/fam-parser example.fam

(Or, if you installed globally using npm install -g, the fam-parser binary should be in your $PATH.)

You can also invoke it directly from the repository root directory without installation:

node javascript/cli.js example.fam

Development of the FAM parser

We use the Python implementation for most of the development as it includes more debugging functionality. Any changes are later lifted to the Javascript implementation.

Preparations

First, make sure that wine is installed and that your CPU allows execution of 16-bit instructions:

echo 1 > /proc/sys/abi/ldt16

Reverse engineering

Run Cyrillic:

wine cyrillic.exe

And start editing a pedigree. Use xxd and watch to find differences:

while true; do watch --differences=permanent xxd pedigree.fam; done

Press Ctrl+c to clear the highlights.

Debugging

If something is wrong, then probably a skipped field is now assumed to be of fixed size, while it should be of variable size. To find the offending field, add the following line to the function _set_field:

print name

The offending field is probably one of the unnamed fields above the one you found, hopefully the nearest one.

Now you can give the unnamed field a name so you can inspect its content.

while true; do
  watch --differences=permanent \
    "fam_parser -d pedigree.fam - | tail -100 | head -50"
done

Vary the values for head and tail to focus on the part of the output you want to inspect.