pyranges.get_fasta

Module Contents

Functions

get_fasta(gr, path)

Get fasta sequence.
pyranges.get_fasta.get_fasta(gr, path)

Get fasta sequence.

Parameters:

  • gr (PyRanges) – Coordinates.

  • path (str) – Path to fasta file

Returns:

Sequences, one per interval.

Return type:

Series

Note

Sorting the PyRanges is likely to improve the speed.

Warning

Note that the names in the fasta header and gr must be the same.

Examples

>>> gr = pr.from_dict({"Chromosome": ["chr1", "chr1"],
...                    "Start": [5, 0], "End": [8, 5]})

>>> gr
+--------------+-----------+-----------+
| Chromosome   |     Start |       End |
| (category)   |   (int32) |   (int32) |
|--------------+-----------+-----------|
| chr1         |         5 |         8 |
| chr1         |         0 |         5 |
+--------------+-----------+-----------+
Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes.
For printing, the PyRanges was sorted on Chromosome.

>>> tmp_handle = open("temp.fasta", "w+")
>>> _ = tmp_handle.write("> chr1\n")
>>> _ = tmp_handle.write("ATTACCAT")
>>> tmp_handle.close()

>>> seq = pr.get_fasta(gr, "temp.fasta")

>>> seq
0      CAT
1    ATTAC
dtype: object

>>> gr.seq = seq
>>> gr
+--------------+-----------+-----------+------------+
| Chromosome   |     Start |       End | seq        |
| (category)   |   (int32) |   (int32) | (object)   |
|--------------+-----------+-----------+------------|
| chr1         |         5 |         8 | CAT        |
| chr1         |         0 |         5 | ATTAC      |
+--------------+-----------+-----------+------------+
Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes.
For printing, the PyRanges was sorted on Chromosome.