biocantor.io.bed.bed

BED comes in a handful of flavors: BED3, BED6, BED12, and BED12+.

The 12 defined columns are:

  1. chrom: Sequence.

  2. start: 0-based start.

  3. end: 0-based exclusive end.

  4. name: A name.

  5. score: A score. Should be an integer between 0 and 1000.

  6. strand: A string. Any of [+, -, .].

  7. thickStart: Translation start site.

  8. thickEnd: Translation end site.

  9. itemRgb: String encoded tuple for an RGB value to display.

  10. blockCount: Number of spliced blocks.

  11. blockSizes: Length of each block.

  12. BlockStarts: Start of each block relative to start.

BED3 is the first 3 columns, BED6 is the first 6, and BED12 is the full thing.

BED12+ basically is just people tacking on extra self-defined columns.

These representations cannot be present in the same file. For this reason, we have separate subclasses for each type that only return their own type.

Module Contents

Classes

RGB

BED3

BED3 includes basic interval information; the simplest type of interval

BED6

BED6 includes name, score and strand information. Cannot be spliced.

BED12

BED12 contains splicing and CDS information. It does not contain frame/phase information.
class biocantor.io.bed.bed.RGB
r :int = 0
g :int = 0
b :int = 0
__str__() → str

Return str(self).

class biocantor.io.bed.bed.BED3

BED3 includes basic interval information; the simplest type of interval

chrom :str
start :int
end :int
__str__() → str

Return str(self).

class biocantor.io.bed.bed.BED6

Bases: BED3

BED6 includes name, score and strand information. Cannot be spliced.

name :str
score :int
strand :inscripta.biocantor.location.Strand
__str__() → str

Return str(self).

class biocantor.io.bed.bed.BED12

Bases: BED6

BED12 contains splicing and CDS information. It does not contain frame/phase information.

thick_start :int
thick_end :int
item_rgb :RGB
block_count :int
block_sizes :List[int]
block_starts :List[int]
__str__() → str

Return str(self).