Combined genome/gene profile allowing stratification

[qiyunzhu]

It is possible to add the following function, which generates a feature table, in which a feature ID contains both genome and gene information, like G000123456|789 (the 789th gene of genome G000123456). This table will enable collapse with either taxonomic or functional classification, or both (i.e., stratified). With this table, one no longer needs to split taxonomic and functional analyses, and there is no need to generate the read mapping intermediate. This file allows the maximum flexibility.

To implement this function, the following modifications need to be made:

1. Modify the ordinal module to allow it output G000123456|789-style features. This is not a simple format change. The code needs to return the genome even there is no matching gene (like G000123456).
2. Add a parameter (or two) to the collapse command, to let it operate on n-th field of a feature ID. For example in this case, 1st field is genome (G000123456), 2nd field is gene (789).