Relate Batch

Each batch of relation vectors is a RelateBatchIO object.

Relate batch: Structure

The following attributes encode the relationships between each read and each position in the reference sequence:

Attribute

Data Type

Description

end5s

numpy.ndarray[int]

array of the first position of the most upstream mate in each read

mid5s

numpy.ndarray[int]

array of the first position of the most downstream mate in each read

mid3s

numpy.ndarray[int]

array of the last position of the most upstream mate in each read

end3s

numpy.ndarray[int]

array of the last position of the most downstream mate in each read

muts

dict[int, dict[int, numpy.ndarray[int]]]

array of the reads with each type of mutation at each position

Note

The positions of the first and last bases in the reference sequence are defined to be 1 and the length of the sequence, respectively.

Relate batch: Structure of read numbers

Each read, or pair of paired-end reads, is labeled with a non-negative integer: 0 for the first read in each batch, and incrementing by 1 for each subsequent read. Within one batch, all read numbers are unique. However, two different batches can have reads that share numbers.

Relate batch: Structure of 5’ and 3’ end positions

  • end5s, mid5s, mid3s, and end3s are all 1-dimensional numpy.ndarray objects.

  • For any relate batch, end5s, mid5s, mid3s, and end3s all have the same length (which may be any integer ≥ 0).

  • A read with index i corresponds to the ith values of end5s, mid5s, mid3s, and end3s; denoted (respectively) end5s[i], mid5s[i], mid3s[i], and end3s[i].

  • For every read i:

    • 1 ≤ end5s[i] ≤ end3s[i] ≤ length of reference sequence

    • If paired-end and there is a gap of ≥ 1 nt between mates 1 and 2:

      • end5s[i] ≤ mid3s[i] < mid5s[i] ≤ end3s[i]

    • Otherwise:

      • end5s[i] = mid5s[i] ≤ mid3s[i] = end3s[i]

Relate batch: Structure of mutations

muts is a dict wherein

  • each key is a position in the reference sequence (int)

  • each value is a dict wherein

    • each key is a type of mutation (int, see Relation Vectors for more information)

    • each value is an array of the numbers of the reads that have the given type of mutation at the given position (numpy.ndarray)

Relate batch: Example

For example, suppose that the reference sequence is TCAGAACC and a batch contains five paired-end reads, numbered 0 to 4:

Read

Mate

Alignment

0

1

_CAG____

0

2

_____AGC

1

1

___GTA__

1

2

TCT_____

2

1

____AAC_

2

2

_CA_____

3

1

TAAGT___

3

2

______CC

4

1

__AGA___

4

2

___GA-C_

Ref

TCAGAACC

The positions, reads, and relationships can be shown explicitly as a matrix (see Relation Vectors for information on the relationship codes):

Read

1

2

3

4

5

6

7

8

0

255

1

1

1

255

1

64

1

1

1

1

128

1

128

1

255

255

2

255

1

1

255

1

1

1

255

3

1

16

1

1

128

255

1

1

4

255

255

1

1

3

3

1

255

In a relate batch, they would be encoded as follows:

  • end5s: [2, 1, 2, 1, 3]

  • mid5s: [4, 1, 3, 5, 3]

  • mid3s: [6, 6, 5, 7, 7]

  • end3s: [8, 6, 7, 8, 7]

  • muts:

    {1: {},
 2: {16: [3]},
 3: {128: [1]},
 4: {},
 5: {3: [4], 128: [1, 3]},
 6: {3: [4]},
 7: {64: [0]},
 8: {}}

    Note that the numbers are shown here for visual simplicity as list objects, but would really be numpy.ndarray objects.