bedparse.bedline module

class bedparse.bedline.bedline(line=None)

Bases: object

The bedline class defines an object that represents a single BED[3,4,6,12] line

Parameters:line (list) – List where each element corresponds to one field of a BED file
bed12tobed6(appendExN=False, whichExon='all')

Returns a list of bedlines (bed6) corresponding to the exons.

Parameters:
  • appendExN (bool) – Appends the exon number to the transcript name
  • whichExon (str) – Which exon to return. One of [“all”, “first”, “last”]. First and last respectively report the first or last exon relative to the TSS (i.e. taking strand into account).
Returns:

list of bedline objects, one per exon
Return type:

list

Examples

>>> bl = bedline(["chr1", 100, 420, "Name", 0, "+", 210, 310, ".", 4, "20,20,20,20,", "0,100,200,300,"])
>>> for i in bl.bed12tobed6(appendExN=True): print(i)
...
['chr1', 100, 120, 'Name_Exon001', 0, '+']
['chr1', 200, 220, 'Name_Exon002', 0, '+']
['chr1', 300, 320, 'Name_Exon003', 0, '+']
['chr1', 400, 420, 'Name_Exon004', 0, '+']
cds(ignoreCDSonly=False)

Return the CDS of a coding transcript. Transcripts without CDS are not reported

Parameters:ignoreCDSonly (bool) – If True return None when the entire transcript is CDS
Returns:The CDS as a bedline object
Return type:bedline

Examples

>>> bl = bedline(["chr1", 100, 500, "Tx1", 0, "+", 200, 300, ".", 1, "400,", "0,"])
>>> print(bl.cds())
['chr1', 200, 300, 'Tx1', 0, '+', 200, 300, '.', 1, '100,', '0,']
introns()

Returns a bedline object of the introns of a transcript

Returns:The introns of the transcripts as a bedline object
Return type:bedline

Examples

>>> bl = bedline(["chr1", 100, 420, "Name", 0, "+", 210, 310, ".", 4, "20,20,20,20,", "0,100,200,300,"])
>>> print(bl.introns())
['chr1', 120, 400, 'Name', 0, '+', 120, 120, '.', 3, '80,80,80,', '0,100,200,']
>>> bl = bedline(["chr1", 100, 420, "Name", 0, "-", 210, 310, ".", 1, "320,", "0,"])
>>> print(bl.introns())
None
pprint()

Prints a bedline object formatted as a python list

print(end='\n')

Prints a bedline object

Parameters:end – Line terminator character
promoter(up=500, down=500, strand=True)

Returns the promoter of a bedline object

Parameters:
  • up (int) – Number of upstream bases
  • down (int) – Number of donwstream bases
  • strand (bool) – If false strandedness is ignored
Returns:

The promoter as a bedline object
Return type:

bedline

Examples

>>> bl = bedline(['chr1', 1000, 2000, 'Tx1', '0', '+'])
>>> print(bl.promoter())
['chr1', 500, 1500, 'Tx1']
translateChr(assembly, target, suppress=False, ignore=False, patches=False)

Convert the chromosome name to Ensembl or UCSC

Parameters:
  • assembly (str) – Assembly of the BED file (either hg38 or mm10).
  • target (str) – Desidered chromosome name convention (ucsc or ens).
  • suppress (bool) – When a chromosome name can’t be matched between USCS and Ensembl set it to ‘NA’ (by default throws as error)
  • ignore (bool) – When a chromosome name can’t be matched between USCS and Ensembl do not report it in the output (by default throws an error)
  • patches (bool) – Allows conversion of all patches up to p11 for hg38 and p4 for mm10. Without this option, if the BED file contains contigs added by a patch the conversion terminates with an error (unless the -a or -s flags are present
Returns:

A bedline object with the converted chromosome
Return type:

bedline

Examples

>>> bl = bedline(['chr1', 1000, 2000, 'Tx1', '0', '-'])
>>> print(bl.translateChr(assembly="hg38", target="ens"))
['1', 1000, 2000, 'Tx1', '0', '-']
>>> bl = bedline(['chr19_GL000209v2_alt', 1000, 2000, 'Tx1', '0', '-'])
>>> print(bl.translateChr(assembly="hg38", target="ens"))
['CHR_HSCHR19KIR_RP5_B_HAP_CTG3_1', 1000, 2000, 'Tx1', '0', '-']
tx2genome(coord, stranded=False)

Given a position in transcript coordinates returns the equivalent in genome coordinates. The transcript coordinates are considered without regard to strand, i.e. 0 is the leftmost position for both + and - strand transcripts, unless the stranded options is set to True.

Parameters:
  • coord (int) – Coordinate to convert from transcript-space to genome space
  • stranded (bool) – If True use the rightmost base of negative strand trascripts as 0
Returns:

Coordinate in genome-space
Return type:

int

Examples

>>> bl = bedline(['chr1', 1000, 2000, 'Tx1', '0', '-'])
>>> bl.tx2genome(10)
1010
>>> bl.tx2genome(10, stranded=True)
1989
utr(which=None)

Returns the UTR of coding transcripts (i.e. those with a CDS)

Parameters:which (int) – Which UTR to return: 3 for 3’UTR or 5 for 5’ UTR
Returns:The UTR as a bedline object
Return type:bedline

Examples

>>> bl = bedline(["chr1", 100, 500, "Tx1", 0, "+", 200, 300, ".", 1, "400,", "0,"])
>>> print(bl.utr(which=5))
['chr1', 100, 200, 'Tx1', 0, '+', 100, 100, '.', 1, '100,', '0,']