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csw / bioruby-maf

MAF parser for BioRuby
MIT License
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Do not return blocks with no sequences #87

Closed csw closed 12 years ago

csw commented 12 years ago

This sort of conflicts with the logic for verifying that we've parsed all the blocks we were supposed to parse from #fetch_blocks. Also, maybe we need to revisit the sequence filtering semantics—does it make sense to be able to filter out the reference sequence? What if we have a block with only one sequence in it? maf_limit_to_species.py doesn't do special handling for the ref seq but only writes out blocks with > 1 component.

csw commented 12 years ago

OK, so, iff sequence_filter is set, filter out any blocks with < 2 sequences.