#1 Compatible issue with different sources and formats of genome annotation

[liangc_mu]

For mapped read cataloging function, we need to consider the compatibility for both NCBI and ENSEMBL gene annotation, either in GTF, GFF or GFF3 format. Please do some investigation about the differences and come up a solution. Perhaps, we can consider adding two more parameters for mirpro_feature_pro:

(1) -src: source of genome annotation, with value of [ncbi|ensembl...]
(2) -format: format of genome annotation, with value of [gtf|gff|gff3|...]

Obviously, the solution of this will depend on HTSeq's capability. Alternatively, we can use some open-source codes that can do conversion among GTF, GFF or GFF3. That might be an alternative solution here.

[liangc_mu]

In the version of 20150930, mipro_feature_pro is capable to accept input files in GFF3 and GTF format.