FAN-C builds extensively on the
genomic_regions package, which provides a unified
interface for most types of region-based genomic data. We highly recommend
reading the documentation
of that package before going into the details of FAN-C, as many of the concepts discussed
therein are central to the handling of data in FAN-C.
You can check whether a FAN-C object supports the
import genomic_regions as gr isinstance(o, gr.RegionBased) # True for objects supporting the regions interface
The current list of FAN-C objects supporting the
Any object built on that foundation supports, for example, region iterators:
for region in hic.regions: print(region) print(region.chromosome, region.start, region.end, region.strand) print(region.is_forward) print(region.center) # ...
for region in hic.regions('chr1:3mb-12mb'): print(region.chromosome) # chr1 # ...
and many more convenient features. The object type returned by all of those queries
GenomicRegion, which has many convenient functions to
deal with region properties and operations.
len(region) # returns the size of the region in base pairs region.center # returns the base (or fraction of base) at the center of the region region.five_prime # returns the starting base at the 5' end of the region region.three_prime # returns the starting base at the 3' end of the region region.is_forward() # True if strand is '+' or '+1' region.is_reverse() # True if strand is '-' or '-1' region.attributes # return all attribute names in this region object region.copy() # return a shallow copy of this region region.to_string() # return a region identifier string describing the region region = gr.as_region('chr12:12.5Mb-18Mb') region.overlaps('chr12:11Mb-13Mb') # True region.overlaps('chr12:11Mb-11.5Mb') # False region.overlaps('chr1:11Mb-13Mb') # False
Refer to the genomic_regions documentation for all the details.
Similarly to the
regions interface for handling collections of genomic regions,
FAN-C implements interfaces for working with pairs of genomic regions (
and matrix operations (
matrix). These work in exactly the same way for FAN-C,
Cooler, and Juicer files. Hence, all of these are directly compatible with FAN-C architectural
functions such as the insulation score or AB compartment analyses, …
These interfaces will be introduced in the following sections, starting with RegionPairsContainer.