Added Sequence method to Feature object #26
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Adds a method to Feature known as Sequence. This was added anticipating the codon optimization feature in #11, which will require parsing codons from features to build codon tables. Additionally, added manually edited test file t4_intron and fixed one bug in io.go.
This commit adds degenerate bases and makes a public method for ReverseComplement, as the full functionality for reverse complementation was previously split in the getSeq function and reverseComplement, which has been renamed to reverseBase. Degenerate base pairs were added using the table from http://arep.med.harvard.edu/labgc/adnan/projects/Utilities/revcomp.html .
Removed most single or double letter variable names and replaced with more human reable names.
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@Koeng101 please review then I'll review again and merge! |
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This pull request adds a minimally viable way to get the sequence of features. This can be used to fill codon tables for optimization, or to just get the DNA sequence of features.
Testing is currently blocked with bug #24 .
Definitely needs some improvement, but as-is it works for the following from this page (basically, all the Location types that are relevant for CDSs): http://www.insdc.org/files/feature_table.html#3.4.3
Usage: