1. Installation instructions¶

metamap requires :

• python
• graphviz : http://www.graphviz.org
• a python binding to graphviz called yapgvb: https://code.google.com/p/yapgvb/
• networkx : https://networkx.github.io/

Once these are installed, you can get metamap by :

• downloading the package file in the Files (or Fichiers) tab above.
• extracting it: tar -xvzf metamap-1.0.tar.gz
• running python setup.py install as root

2. Running metamap¶

metamap is made to run on a file obtained by running the mcmc command in carthagene.
typing metamap -h gives the list of available options:

$ metamap -h

***** This is METAMAP v1.0 ******

Usage: metamap [options] input_file

Options:
  -h, --help            show this help message and exit
  -2, --2pt             Use 2-point probability distribution
  -R ROBUSTFILE, --robust=ROBUSTFILE
                        Build a robust (framework) map from the metamap and
                        store results in ROBUSTFILE
  -i T, --include-threshold=T
                        Include a group in the robust map if best order has
                        posterior probability > T (default 0.999)
  -l FILE, --load=FILE  Load Results from FILE
  -m I, --ref-map=I     Use map number I as reference map
  -M FILE, --marker-list=FILE
                        Consider only markers listed in FILE
  -n N, --nmaps=N       Read the first N maps of the distribution
  -p PREFIX, --prefix=PREFIX
                        use PREFIX for output files
  -r, --reverse         Reverse all maps
  -S, --stats           Output simple statistics on the metamap
  -t T (default 0.999), --seq-threshold=T (default 0.999)
                        Build initial marker sequences with threshold T