The following helper scripts are attached to this page and you may find them useful when creating the alignment definition files:
The usual pipeline is:
Takes a sample XML format (you may want do modify this part of the script), two encoded corporaand the name of the mapping structure attribute. It looks up the structure ID in both corporaaccording to the attribute values in the XML file and produces alignment definition file. The output should be processed by fixgaps.py and compressrng.py.
Takes two alignment definition files L2-L1 and L3-L1 and computes a new one L2-L3. The output should be processed by fixgaps.py and compressrng.py.
Inserts empty alignment into an existing alignment file where gaps are found.
Compresses subsequent empty alignments into one range. May significantly reduce the size of an alignment definition file.