Mapper

A utility for mapping a genomic coordinate to a specific position in a corresponding CDS or AA sequence.

Requirements

• refFlat.txt file - UCSC annotation file specific to each species
• RefSeq ID - mRNA RefSeq Identifier (ex NM_146145)
• Genomic Coordinate - nucloetide location on chromosome (ex 101153495)

Uses

Command Line Tool:

./mapper.py NM_146145 101153495 data/refFlatMm10.txt

Python Object:

from mapper import Mapper

mapper = Mapper("data/refFlatMm10.txt")
cds_pos, aa_pos = mapper.map(101153495, "NM_146145")

Tested using Python 2.7 and Python 3.5