This is a script that uses MA-PRALINE to prepare simultaneous MSA jobs. Currently, the jobs are run in-process, but they will eventually be sent to a cluster where they will be run in parallel.
The script, wgt.py, takes a single argument, which contains the path to a job
file in JSON format. This file contains an list of lists, with each outer list
item corresponding to a job and each inner list item corresponding to a
component of a command-line option. See the example in input/test.json for
more details.
The interesting part of the script is the do_multiple_sequence_alignments
function, which takes a list of msa_input objects, and returns a list of
alignment objects containing the finished alignments for all the jobs. It is
here where the jobs should be sent off to Constellation.
Support was also added to specify a predetermined join order tree in Newick
format, through the --tree-file option. If this option is not specified
MA-PRALINE will determine the join order itself through normal means. This was
used for debugging, but if it complicates the logic it can safely be removed.