The bed12 module

Defines a set a generic function to parse and process bed12 files.

umicount.bed12.blocks_to_absolute_start_end(read)

Calculate the absolute start and end of the blocks from a bed12 line.

Args:

read: A list of twelve elements where each element refers to a field in the BED format.

Returns:

A list of tuple where each tuple contains the absolute start and end coordinates of a block.

>>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
>>> blocks_to_absolute_start_end(read)
[(100, 121), (175, 200)]

umicount.bed12.get_chrom(read)

Get chromosome from a bed12 line.

Args:

read: A list of twelve elements where each element refers to a field in the BED format.

Returns:

The chromosome name

>>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
>>> get_chrom(read)
'chrX'

umicount.bed12.get_end(read)

Get end position from a bed12 line.

Args:

read: A list of twelve elements where each element refers to a field in the BED format.

Returns:

An integer representing the end position of the read.

>>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
>>> get_end(read)
200

umicount.bed12.get_start(read)

Get start position from a bed12 line.

Args:

read: A list of twelve elements where each element refers to a field in the BED format.

Returns:

An integer representing the start position of the read.

>>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
>>> get_start(read)
100

umicount.bed12.get_strand(read)

Get strand from a bed12 line.

Args:

read: A list of twelve elements where each element refers to a field in the BED format.

Returns:

A single char representing the strand of a read

>>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
>>> get_strand(read)
'+'

umicount.bed12.get_tss(read)

Get Transcription Start Site (TSS) from a bed12 line.

Args:

read: A list of twelve elements where each element refers to a field in the BED format.

Returns:

The start position as an integer if the read is on the plus strand. The end position as an integer if the read is on the minus strand.

>>> read = ['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '21,25', '0,75']
>>> get_tss(read)
100
>>> read = ['chrX', '100', '200', 'toto', '12', '-', '100', '110', '255,0,0', '2', '21,25', '0,75']
>>> get_tss(read)
200

umicount.bed12.merge_overlapping_blocks(reads)

Merge blocks if they overlap.

Args:

reads: A list of read in the BED12 format.

Returns:

Two lists where the first list contains the blocks sizes and the second the blocks starts. Values in the lists are integer.

>>> reads = []
>>> reads.append(['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '2', '20,25', '0,75'])
>>> reads.append(['chrX', '100', '200', 'toto', '12', '+', '100', '110', '255,0,0', '3', '10,10,25', '0,15,75'])
>>> merge_overlapping_blocks(reads)
([25, 25], [0, 75])