pyigd Documentation
Contents:
pyigd is a Python library for reading and writing Indexable Genotype Data (IGD) files. IGD is a binary format that is very simple and uses no compression, but tends to be quite small and fast.
IGDReader example
Example of how to read an IGD file. See pyigd.IGDReader for the relevant API reference.
import pyigd
import sys
if len(sys.argv) < 2:
print("Pass in IGD filename")
exit(1)
with open(sys.argv[1], "rb") as f:
igd_file = pyigd.IGDReader(f)
print(f"Version: {igd_file.version}")
print(f"Ploidy: {igd_file.ploidy}")
print(f"Variants: {igd_file.num_variants}")
print(f"Individuals: {igd_file.num_individuals}")
print(f"Source: {igd_file.source}")
print(f"Description: {igd_file.description}")
for variant_index in range(igd_file.num_variants):
print(f"REF: {igd_file.get_ref_allele(variant_index)}, ALT: {igd_file.get_alt_allele(variant_index)}")
position, is_missing, sample_list = igd_file.get_samples(variant_index)
print( (position, is_missing, len(sample_list)) )
IGDWriter example
Example of how to write an IGD file. See pyigd.IGDWriter for the relevant API reference. Some of the methods invoked have a required order, and in general all the variants (sample info) needs to be written immediately after the header. The IGDWriter maintains some state, and for large datasets can use a non-trivial amount of RAM to maintain indexes while writing variant data.
num_individuals = 100
with open("output.igd", "wb") as f:
w = IGDWriter(f, num_individuals)
w.write_header()
w.write_variant(100, "A", "G", [1, 22, 99, 101])
w.write_variant(101, "A", "C", list(range(200)))
w.write_index()
w.write_variant_info()
w.write_individual_ids([]) # optional
w.write_variant_ids([]) # optional
# We write the header twice because the IGDWriter is updating fields
# on the header as we call the other methods above. For example, it is
# counting the number of variants being written and that gets updated
# in the header the second time we write it.
f.seek(0)
w.write_header()