csw/bioruby-maf — pull request #52 by csw (2012-06-29 19:15:25+00:00)
Title: Remove gaps after filtering species

It should be possible to filter sequences to obtain only certain species, and then remove all-gap columns in the resulting alignment blocks.

Species filtering is [already implemented](http://rubydoc.info/github/csw/bioruby-maf/#Filter_species_returned_in_alignment_blocks). This branch adds a `Block#remove_gaps!` method with 3eff1f63. It also adds `Block#filtered?` to detect blocks which have been modified by the filter and are thus candidates for having `#remove_gaps` called on them.

Does this look like it would do the right thing? See the tests for `Block#remove_gaps!` with reference to the first block of [mm8_chr7_tiny.maf](https://github.com/csw/bioruby-maf/blob/master/test/data/mm8_chr7_tiny.maf).

I can build this into a higher-level script; would this be useful in the context of extracting blocks from specific genomic regions, or batch-processing an entire MAF file, or both?