Coordinate mapping

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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.

Configuration

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

Mapping

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.

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