Python Framework For Converting Genomic To Protein Coordinates

Question

[user]

Is there a framework for converting between genomic coordinates and protein coordinates, given a transcript (i.e. a list of exon coordinates)? To go from CDS coordinates to amino-acid coordinates.

The trick is to do this correctly even when the transcript is on the minus strand, which would mean the highest coordinate (not lowest) indicates the start amino acid.

I saw the BioPython related frameworks (like this http://biopython.org/wiki/Coordinate_mapping and this https://gist.github.com/3172753) but I'd prefer not to rely on all of BioPython just for the coordinate transform. I also am not sure how BioPython handles the strandedness.

Apparently PyGr can do this but with ORF containing transcripts but I've never seen an example and cannot see how it can be done from the documentation.

Any pointers to frameworks that do this correctly or examples would be helpful.

Answer 1

[Pierre Lindenbaum]

for the algorithm protein->genomic it using the UCSC knownGene database. see this java code: http://plindenbaum.blogspot.fr/2011/03/mapping-mutation-on-protein-to-genome.html

for the algorithm genomic->protein: see this previous post: How to calculate the protein change and codon position within a nucleotide sequence of a single nucleotide substitution?