genomictools 0.0.7

Tools for processing genomic ranges

genomictools - Tools for processing genomic ranges

The genomictools package provides an easy solution to all data types with a genomic range.

Installation

pip install genomictools

Basic usage

The basic class of a genomic range is called GenomicPos. The start and stop in GenomicPos are all 1-based coordinate.

r = GenomicPos("chr1", 1, 100)
print(str(r), r.name, r.start, r.stop) # "chr1:1-100" "chr1", 1, 100
r = GenomicPos("chr1:1-100")
print(str(r), r.name, r.start, r.stop) # "chr1:1-100" "chr1", 1, 100
r = GenomicPos("chr1:1")
print(str(r), r.name, r.start, r.stop) # "chr1:1-1" "chr1", 1, 1

To avoid confusion, it also provides the way to get 0-based or 1-based coordinate zstart, ostart, zstop, ostop. For example, in BED, we usually have 0-based start coordinate and 1-based stop coordinate.

r = GenomicPos("chr1", 1, 100)
print(r.name, r.zstart, r.ostop) # "chr1" 0 100

To store a list of genomic ranges, we can use GenomicCollection.

from genomictools import GenomicPos, GenomicCollection

r1 = GenomicPos("chr1:1-100")
r2 = GenomicPos("chr3:1000-2000")
r3 = GenomicPos("chr1:51-200")

regions = GenomicCollection([r1, r2, r3])
print(len(regions)) # 3

# When iterating through the regions, they will be sorted by name, start and stop. 
for r in regions: 
	print(str(r))
# chr1:1-100
# chr1:51-200
# chr3:1000-2000

# One can check if a region overlaps any entry within the genomic collection
print(regions.overlaps(GenomicPos("chr1:201-300"))) # False
print(regions.overlaps(GenomicPos("chr1:2-3"))) # True
print(regions.overlaps(GenomicPos("chr2:2-3"))) # False

# One can extract all entries from the genomic collection that overlap with the target region
for r in regions.find_overlaps(GenomicPos("chr1:1-3")):
	print(str(r))
# chr1:1-100
for r in regions.find_overlaps(GenomicPos("chr1:26-75")):
	print(str(r))
# chr1:1-100
# chr1:51-200

For any data entry with an associated genomic range, it will implement GenomicAnnotation, where any GenomicAnnotation instance will have a property genomic_pos

from biodata.bed import BED
bed = BED("chr1", 0, 100, name="R1")
print(str(bed.genomic_pos)) # chr1:1-100

One can use GenomicAnnotation as entries in GenomicCollection.

from biodata.bed import BED
from genomictools import GenomicPos, GenomicCollection

beds = GenomicCollection([BED("chr1", 0, 100, name="R1"), BED("chr3", 1999, 2000, name="R2"), BED("chr1", 50, 200, name="R3")])
for bed in beds:
	r = bed.genomic_pos
	print(bed.name, str(r))
# R1 chr1:1-100
# R3 chr1:51-200
# R2 chr3:2000-2000

for bed in beds.find_overlaps(GenomicPos("chr1:26-75")):
	r = bed.genomic_pos
	print(bed.name, str(r))
# R1 chr1:1-100
# R3 chr1:51-200

The base class of genomic range with strand is StrandedGenomicPos, which extends GenomicPos.

For any data entry with an associated stranded genomic range, it will implement StrandedGenomicAnnotation, where any StrandedGenomicAnnotation instance will have properties stranded_genomic_pos and genomic_pos. The strand should be + for positive strand, - for negative strand and . for unspecified strand.

from biodata.bed import BED
bed = BED("chr1", 0, 100, name="R1", strand="-")
print(str(bed.stranded_genomic_pos)) # chr1:1-100:-
print(str(bed.genomic_pos)) # chr1:1-100

One could also use GenomicCollection to store genomic ranges data easily:

from biodata.bed import BEDReader
from genomictools import GenomicCollection
beds = BEDReader.read_all(GenomicCollection, filename)