Contributed by Lenna X. Peterson
Mapping genetic locations between different coordinate systems is an essential part of much genomic analysis. This is a brief introduction to the SeqMapper module.
Note: This uses the coordinate mapper currently available on my branch. This in turn is a branch of Peter's branch introducing CompoundLocations. It will not work with the old style of SeqFeature.
The mapper and mapping positions store all positions in Python coordinates, i.e. 0-based. Many users are working with data that is 1-based, such as GenBank or HGVS. Each map position type has a "to_hgvs" and "to_genbank" method for easy conversion. It is also possible to set the default print representation of mapping positions to either of these formats:
from Bio.SeqUtils.Mapper import MapPosition def use_genbank(self): return str(self.to_genbank()) MapPosition.__str__ = use_genbank
The first step to using the mapper is to get the exons from a GenBank or similar file. The mapper will accept exons as a sequence of pairs, a SeqRecord with a CDS feature, or a CDS SeqFeature. The file used in this example is located in the Tests directory of the Biopython source code.
from Bio.SeqUtils.Mapper import CoordinateMapper from Bio import SeqIO def get_first_CDS(parser): for rec in parser: for feat in rec.features: if feat.type == "CDS" and len(feat.location.parts) > 1: return feat exons = get_first_CDS(SeqIO.parse("GenBank/cor6_6.gb", "genbank")) cm = CoordinateMapper(exons)
Once the mapper is constructed, its methods can be used to transform positions located within the given CDS. Note that attempting to transcribe and translate a genomic position that is not within CDS will raise an exception. Also note that printing the list will show the repr of the positions, which are in Python 0-based coordinates.
sample_g_values = [50, 150, 250, 350, 450, 550, 650] protein_positions =  for raw_g_pos in sample_g_values: # EAFP method try: # Dialect argument converts g_pos from Genbank to Python coordinates p_pos = cm.g2p(raw_g_pos, dialect="genbank") except ValueError: p_pos = None protein_positions.append(p_pos) print protein_positions
Here's an example function that prints a table of the genomic, CDS, and protein coordinates given a coordinate mapper and a list of genomic values.
from Bio.SeqUtils.Mapper import GenomePosition def gcp_table(mapper, g_list): """Print a table of genomic, CDS, and protein coordinates""" # Print header print "%4s | %6s | %2s" % ("g", "CDS", "p") print "-" * 20 for g_pos in g_list: # Directly convert g_pos from Genbank to Python coordinates g_pos = GenomePosition.from_dialect("genbank", g_pos) c_pos = mapper.g2c(g_pos) # LBYL method: if c_pos.pos_type == "exon": p_pos = mapper.c2p(c_pos) else: p_pos = "" # Print formatted row print "%4s | %6s | %2s" % (g_pos, c_pos, p_pos) gcp_table(cm, sample_g_values)
The code shown in this example may be downloaded here: https://gist.github.com/lennax/10600113 The example file used is located in the Tests directory of the Biopython source code.