BedContainer Class

Represents a Bed Storage for BedEntry objects.

BedContainer Class (BedEntry 3 Col)

class bedContainer.BedContainer.BedContainer(addExtras: bool = False)

Represents a Python Container for BedEntry objects (bed file format rows with 3 columns, plus possibly Extra Fields).

__init__(addExtras: bool = False) → None

Creates an instance of BedEntry object.

Parameters:addExtras (bool) – True if the Bed Entries have extra fields, False otherwise.
empty() → None

Remove all BedEntries in the BedContainer. Also, reset all Counters. Final result similar to a new BedContainer instance.

select_Chromosomes() → List[str]

Returns all chromosome names present in the BedContainer

Return List:Return a List of strings representing chromosome names.
select_EntriesInChr(chrom: str) → List[bedEntry.BedEntry.BedEntry]

Returns all BedEntry objects inside the BedContainer, in the specified chromosome.

If none, an empty list is returned.

Parameters:chrom (str) – Chromosome name (chr) of BedEntry objects to return
Return List:A List of all BedEntry located in chrom
number_EntriesInChr(chrom: str) → int

Number of BedEntry with input chromosome name.

If none, 0 (zero) ir returned.

Parameters:chrom (str) – Chromosome name (chr) of BedEntry objects to count
Returns:Number of BedEntry with input chromosome name.
addFrom_List(listBedEntry: List[Union[str, List[T]]]) → None
Add one BedEntry object based in input list (listBedEntry), composed by strings / List, following the rules below:
[“chr”, “sCoord”, “eCoord”, [extraField1, extraField2, …]] (extraFields List is optional)

This function is also responsible for adding a unite to entryCounts Counter and to reset the sort property of BedContainer to False, since the new added BedEntry is added at the end of the correspondent chromosome list. Besides that, it also ensured that the chromosome key of the new BedEntry is added to the BedContainer if not already there.

Parameters:listBedEntry (List) – A list of strings with the required properties to be initialized by BedEntry constructor.
addFrom_BedEntryObj(obj: bedEntry.BedEntry.BedEntry) → None

Add BedEntry object directly in the container.

This function is also responsible for adding a unite to entryCounts Counter and to reset the sort property of BedContainer to False, since the new added BedEntry is added at the end of the correspondent chromosome list. Besides that, it also ensured that the chromosome key is added to the BedContainer if not already there.

Parameters:obj (BedEntry) – BedEntry object to add.
removeEntryBed(entryBedObj: bedEntry.BedEntry.BedEntry) → None

Remove BedEntry object from BedContainer.

This function is also responsible for decrease one unite to entryCounts Counter and ensured that the chromosome key is removed from BedContainer if not there is no BedEntry in that chromosome.

Parameters:entryBedObj (BedEntry) – BedEntry object to remove
static merge(other1: object, other2: object) → object

Returns a their BedContainer object, with the content of the both merged input BedContainer*s. Having as great advantage the preservation of *BedEntry objects inside the input BedContainer objects.

If at least one input BedContainer has flagged having extraField (addExtras), it ensures that the final BedContainer output also has that flag as True.

Parameters:
Returns:

Returns a their BedContainer object, with the content of both input ones.
sort() → None

Sort the list of each chromosome in the bedContainer recursively and the Chromosome List (chrList). Ensures that set the sorted flag to True

readFromBedFile(BedFilePath: str) → None

Read a Bed File with 3 Columns (is possible to add more in extraFields) and store in the BedContainer object.

Parameters:BedFilePath (str) – Path to Bed File Format
writeToBedFile(BedFilePath: str) → None

Writes in a Bed File Format all BedEntry objects inside BedContainer. If the BedContainer has defined having the flag addExtras as True, the extra fields will also be write in the Bed File, in the same order as they are registered in BedContainer object.

Parameters:BedFilePath (str) – The path where the bed file will be writen.

Build-in Functions

BedContainer.__getitem__(item: int) → bedEntry.BedEntry.BedEntry

Getter item function for BedContainer class. Design to return a single BedEntry per time. Slices are not accepted, by now.

Parameters:item (int) – Index of BedEntry to retrieve
Return BedEntry:
 A BedEntry Object(s)
BedContainer.__iter__() → Generator[bedEntry.BedEntry.BedEntry, None, None]

Iterator function for BedContainer class.

Return BedEntry:
 A BedEntry Object
BedContainer.__len__()

Returns the number of BedEntry objects in the BedContainer

Returns:Number BedEntry objects
BedContainer.__eq__()

Return self==value.

BedContainer.__str__()

A meta representation of the BedContainer

The following parameters are being returned:

  • Number of Entries
  • Number Chromosomes
  • isSorted (Flag)
  • Add Extra Fields (Flag)
Returns:String with the BedContainer meta representation.

BedContainer Class (6 Col)

class bedContainer.BedContainer6.BedContainer6(addExtras: bool = False)

Bases: bedContainer.BedContainer.BedContainer

Represents a Python Container for BedEntry6 objects (bed file format rows with 6 columns, plus possibly Extra Fields).

__init__(addExtras: bool = False)

Creates an instance of BedEntry object.

Parameters:addExtras (bool) – True if the Bed Entries have extra fields, False otherwise.
addFrom_List(listBedEntry: List[Union[str, List[T], int]]) → None
Add one BedEntry object based in input list (listBedEntry), composed by strings / List, following the rules below:
[“chr”, “sCoord”, “eCoord”, “name”, “score”,”strand”, [extraField1, extraField2, …]] (extraFields List is optional)

This function is also responsible for adding a unite to entryCounts Counter and to reset the sort property of BedContainer to False, since the new added BedEntry is added at the end of the correspondent chromosome list. Besides that, it also ensured that the chromosome key of the new BedEntry is added to the BedContainer if not already there.

Parameters:listBedEntry (List) – A list of strings with the required properties to be initialized by BedEntry constructor.
addFrom_BedEntryObj(obj: bedEntry.BedEntry.BedEntry) → None

Add BedEntry object directly in the container.

This function is also responsible for adding a unite to entryCounts Counter and to reset the sort property of BedContainer to False, since the new added BedEntry is added at the end of the correspondent chromosome list. Besides that, it also ensured that the chromosome key is added to the BedContainer if not already there.

Parameters:obj (BedEntry) – BedEntry object to add.
empty() → None

Remove all BedEntries in the BedContainer. Also, reset all Counters. Final result similar to a new BedContainer instance.

static merge(other1: object, other2: object) → object

Returns a their BedContainer object, with the content of the both merged input BedContainer*s. Having as great advantage the preservation of *BedEntry objects inside the input BedContainer objects.

If at least one input BedContainer has flagged having extraField (addExtras), it ensures that the final BedContainer output also has that flag as True.

Parameters:
Returns:

Returns a their BedContainer object, with the content of both input ones.
number_EntriesInChr(chrom: str) → int

Number of BedEntry with input chromosome name.

If none, 0 (zero) ir returned.

Parameters:chrom (str) – Chromosome name (chr) of BedEntry objects to count
Returns:Number of BedEntry with input chromosome name.
readFromBedFile(BedFilePath: str) → None

Read a Bed File with 3 Columns (is possible to add more in extraFields) and store in the BedContainer object.

Parameters:BedFilePath (str) – Path to Bed File Format
removeEntryBed(entryBedObj: bedEntry.BedEntry.BedEntry) → None

Remove BedEntry object from BedContainer.

This function is also responsible for decrease one unite to entryCounts Counter and ensured that the chromosome key is removed from BedContainer if not there is no BedEntry in that chromosome.

Parameters:entryBedObj (BedEntry) – BedEntry object to remove
select_Chromosomes() → List[str]

Returns all chromosome names present in the BedContainer

Return List:Return a List of strings representing chromosome names.
select_EntriesInChr(chrom: str) → List[bedEntry.BedEntry.BedEntry]

Returns all BedEntry objects inside the BedContainer, in the specified chromosome.

If none, an empty list is returned.

Parameters:chrom (str) – Chromosome name (chr) of BedEntry objects to return
Return List:A List of all BedEntry located in chrom
sort() → None

Sort the list of each chromosome in the bedContainer recursively and the Chromosome List (chrList). Ensures that set the sorted flag to True

writeToBedFile(BedFilePath: str) → None

Writes in a Bed File Format all BedEntry objects inside BedContainer. If the BedContainer has defined having the flag addExtras as True, the extra fields will also be write in the Bed File, in the same order as they are registered in BedContainer object.

Parameters:BedFilePath (str) – The path where the bed file will be writen.

Build-in Functions

BedContainer6.__getitem__(item: int) → bedEntry.BedEntry6.BedEntry6

Getter item function for BedContainer class. Design to return a single BedEntry per time. Slices are not accepted, by now.

Parameters:item (int) – Index of BedEntry to retrieve
Return BedEntry:
 A BedEntry Object
BedContainer6.__iter__() → Generator[bedEntry.BedEntry6.BedEntry6, bedEntry.BedEntry6.BedEntry6, None]

Iterator function for BedContainer class.

Return BedEntry:
 A BedEntry Object
BedContainer6.__len__()

Returns the number of BedEntry objects in the BedContainer

Returns:Number BedEntry objects
BedContainer6.__eq__()

Return self==value.

BedContainer6.__str__()

A meta representation of the BedContainer

The following parameters are being returned:

  • Number of Entries
  • Number Chromosomes
  • isSorted (Flag)
  • Add Extra Fields (Flag)
Returns:String with the BedContainer meta representation.