pyTwobit


NamepyTwobit JSON
Version 0.2.0 PyPI version JSON
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home_pagehttps://github.com/jrobinso/pyTwoBit
SummaryA fast reader for local or remote UCSC twobit sequence files.
upload_time2024-09-26 04:13:01
maintainerNone
docs_urlNone
authorJim Robinson
requires_pythonNone
licenseMIT
keywords
VCS
bugtrack_url
requirements requests
Travis-CI No Travis.
coveralls test coverage No coveralls.
            # pyTwoBit

Package for fetching sequence from twobit files from local paths or URLs. 

## Usage

To fetch sequence for a genomic region create a TwoBit object with either a local file path or url.  Sequence
is fetched with the `fetch` function which takes chromosome name, start, and end coordinates.
The UCSC coordinate convention is used (0 start, half-open).


Local file

```python

from pytwobit import TwoBit

twobit = TwoBit('test.2bit')
seq = twobit.fetch("chr1", 50, 57)  # -> "CTATCTA"


```

Remote file

```python

from pytwobit import TwoBit

twobit = TwoBit("https://igv.org/genomes/data/hg38/hg38.2bit")
seq = twobit.fetch("chr1", 120565294, 120565335)  # -> "TATGAACTTTTGTTCGTTGGTgctcagtcctagaccctttt"

```

            

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