stria
a fast Python package for identification and analysis of short tandem repeat sequences
Introduction
A Tandem repeat (TR) in genomic sequence is a set of adjacent short DNA sequence repeated consecutively. The core sequence or repeat unit is generally called motif. According to the motif length, tandem repeats can be classified as microsatellites and minisatellites. Microsatellites are also known as simple sequence repeats (SSRs) or short tandem repeats (STRs) with motif length of 1-6 bp. Minisatellites are also sometimes referred to as variable number of tandem repeats (VNTRs) has longer motif length than micorsatellites.
The stria is a lightweight Python C extension for identification and analysis of short tandem repeats. The stria enables to fastly identify both exact and imperfect SSRs and VNTRs from large numbers of DNA sequences. The stria also provides command line tools for users to extract tandem repeats from Fasta files.
Usage
>>> import stria
>>> import pyfastx
>>> for name, seq, _ in pyfastx.Fastx('test.fa.gz'):
>>> for ssr in SSRMiner(name, seq):
>>> print(ssr.as_string())
Documentation
Metadata
Release files for stria 0.1.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| stria-0.1.3.tar.gz | 14.9 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| stria-0.1.3-pp37-pypy37_pp73-win32.whl | PyPy 3.7 | PyPy 3.7 7.3 | Windows x86-32 | Details |
| stria-0.1.3-pp37-pypy37_pp73-manylinux2010_x86_64.whl | PyPy 3.7 | PyPy 3.7 7.3 | Linux glibc 2.12+ x86-64 | Details |
| stria-0.1.3-pp37-pypy37_pp73-manylinux1_x86_64.whl | PyPy 3.7 | PyPy 3.7 7.3 | Linux glibc 2.5+ x86-64 | Details |
| stria-0.1.3-pp37-pypy37_pp73-macosx_10_9_x86_64.whl | PyPy 3.7 | PyPy 3.7 7.3 | macOS 10.9+ x86-64 | Details |
| stria-0.1.3-pp36-pypy36_pp73-win32.whl | PyPy 3.6 | PyPy 3.6 7.3 | Windows x86-32 | Details |
| stria-0.1.3-pp36-pypy36_pp73-manylinux2010_x86_64.whl | PyPy 3.6 | PyPy 3.6 7.3 | Linux glibc 2.12+ x86-64 | Details |
| stria-0.1.3-pp36-pypy36_pp73-manylinux1_x86_64.whl | PyPy 3.6 | PyPy 3.6 7.3 | Linux glibc 2.5+ x86-64 | Details |
| stria-0.1.3-pp36-pypy36_pp73-macosx_10_9_x86_64.whl | PyPy 3.6 | PyPy 3.6 7.3 | macOS 10.9+ x86-64 | Details |
| stria-0.1.3-cp39-cp39-win_amd64.whl | CPython 3.9 | CPython 3.9 | Windows x86-64 | Details |
| stria-0.1.3-cp39-cp39-win32.whl | CPython 3.9 | CPython 3.9 | Windows x86-32 | Details |
| stria-0.1.3-cp39-cp39-manylinux2010_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.12+ x86-64 | Details |
| stria-0.1.3-cp39-cp39-manylinux2010_i686.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.12+ x86-32 | Details |
| stria-0.1.3-cp39-cp39-manylinux1_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.5+ x86-64 | Details |
| stria-0.1.3-cp39-cp39-manylinux1_i686.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.5+ x86-32 | Details |
| stria-0.1.3-cp39-cp39-macosx_10_9_x86_64.whl | CPython 3.9 | CPython 3.9 | macOS 10.9+ x86-64 | Details |
| stria-0.1.3-cp38-cp38-win_amd64.whl | CPython 3.8 | CPython 3.8 | Windows x86-64 | Details |
| stria-0.1.3-cp38-cp38-win32.whl | CPython 3.8 | CPython 3.8 | Windows x86-32 | Details |
| stria-0.1.3-cp38-cp38-manylinux2010_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.12+ x86-64 | Details |
| stria-0.1.3-cp38-cp38-manylinux2010_i686.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.12+ x86-32 | Details |
| stria-0.1.3-cp38-cp38-manylinux1_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.5+ x86-64 | Details |
| stria-0.1.3-cp38-cp38-manylinux1_i686.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.5+ x86-32 | Details |
| stria-0.1.3-cp38-cp38-macosx_10_9_x86_64.whl | CPython 3.8 | CPython 3.8 | macOS 10.9+ x86-64 | Details |
| stria-0.1.3-cp37-cp37m-win_amd64.whl | CPython 3.7 | CPython 3.7 pymalloc | Windows x86-64 | Details |
| stria-0.1.3-cp37-cp37m-win32.whl | CPython 3.7 | CPython 3.7 pymalloc | Windows x86-32 | Details |
| stria-0.1.3-cp37-cp37m-manylinux2010_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.12+ x86-64 | Details |
| stria-0.1.3-cp37-cp37m-manylinux2010_i686.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.12+ x86-32 | Details |
| stria-0.1.3-cp37-cp37m-manylinux1_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.5+ x86-64 | Details |
| stria-0.1.3-cp37-cp37m-manylinux1_i686.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.5+ x86-32 | Details |
| stria-0.1.3-cp37-cp37m-macosx_10_9_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | macOS 10.9+ x86-64 | Details |
| stria-0.1.3-cp36-cp36m-win_amd64.whl | CPython 3.6 | CPython 3.6 pymalloc | Windows x86-64 | Details |
| stria-0.1.3-cp36-cp36m-win32.whl | CPython 3.6 | CPython 3.6 pymalloc | Windows x86-32 | Details |
| stria-0.1.3-cp36-cp36m-manylinux2010_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.12+ x86-64 | Details |
| stria-0.1.3-cp36-cp36m-manylinux2010_i686.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.12+ x86-32 | Details |
| stria-0.1.3-cp36-cp36m-manylinux1_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.5+ x86-64 | Details |
| stria-0.1.3-cp36-cp36m-manylinux1_i686.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.5+ x86-32 | Details |
| stria-0.1.3-cp36-cp36m-macosx_10_9_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | macOS 10.9+ x86-64 | Details |
| stria-0.1.3-cp35-cp35m-win_amd64.whl | CPython 3.5 | CPython 3.5 pymalloc | Windows x86-64 | Details |
| stria-0.1.3-cp35-cp35m-win32.whl | CPython 3.5 | CPython 3.5 pymalloc | Windows x86-32 | Details |
| stria-0.1.3-cp35-cp35m-manylinux2010_x86_64.whl | CPython 3.5 | CPython 3.5 pymalloc | Linux glibc 2.12+ x86-64 | Details |
| stria-0.1.3-cp35-cp35m-manylinux2010_i686.whl | CPython 3.5 | CPython 3.5 pymalloc | Linux glibc 2.12+ x86-32 | Details |
| stria-0.1.3-cp35-cp35m-manylinux1_x86_64.whl | CPython 3.5 | CPython 3.5 pymalloc | Linux glibc 2.5+ x86-64 | Details |
| stria-0.1.3-cp35-cp35m-manylinux1_i686.whl | CPython 3.5 | CPython 3.5 pymalloc | Linux glibc 2.5+ x86-32 | Details |
| stria-0.1.3-cp35-cp35m-macosx_10_9_x86_64.whl | CPython 3.5 | CPython 3.5 pymalloc | macOS 10.9+ x86-64 | Details |
Total release size: 1.6 MB
Release files / stria-0.1.3.tar.gz
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Release files / stria-0.1.3-pp37-pypy37_pp73-manylinux2010_x86_64.whl
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Release files / stria-0.1.3-pp37-pypy37_pp73-manylinux1_x86_64.whl
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Release files / stria-0.1.3-pp37-pypy37_pp73-macosx_10_9_x86_64.whl
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Release files / stria-0.1.3-pp36-pypy36_pp73-win32.whl
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Release files / stria-0.1.3-pp36-pypy36_pp73-manylinux2010_x86_64.whl
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Release files / stria-0.1.3-pp36-pypy36_pp73-manylinux1_x86_64.whl
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Release files / stria-0.1.3-pp36-pypy36_pp73-macosx_10_9_x86_64.whl
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Release files / stria-0.1.3-cp39-cp39-win_amd64.whl
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Release files / stria-0.1.3-cp39-cp39-manylinux2010_x86_64.whl
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Release files / stria-0.1.3-cp39-cp39-manylinux1_x86_64.whl
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Release files / stria-0.1.3-cp39-cp39-manylinux1_i686.whl
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Release files / stria-0.1.3-cp39-cp39-macosx_10_9_x86_64.whl
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Release files / stria-0.1.3-cp38-cp38-win_amd64.whl
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Release files / stria-0.1.3-cp38-cp38-win32.whl
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Release files / stria-0.1.3-cp38-cp38-manylinux2010_x86_64.whl
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Release files / stria-0.1.3-cp38-cp38-manylinux2010_i686.whl
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Release files / stria-0.1.3-cp38-cp38-manylinux1_x86_64.whl
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Release files / stria-0.1.3-cp38-cp38-manylinux1_i686.whl
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Release files / stria-0.1.3-cp38-cp38-macosx_10_9_x86_64.whl
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Release files / stria-0.1.3-cp37-cp37m-win_amd64.whl
| Download URL | stria-0.1.3-cp37-cp37m-win_amd64.whl |
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Release files / stria-0.1.3-cp37-cp37m-win32.whl
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Release files / stria-0.1.3-cp37-cp37m-manylinux2010_x86_64.whl
| Download URL | stria-0.1.3-cp37-cp37m-manylinux2010_x86_64.whl |
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Release files / stria-0.1.3-cp37-cp37m-manylinux2010_i686.whl
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Release files / stria-0.1.3-cp37-cp37m-manylinux1_x86_64.whl
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Release files / stria-0.1.3-cp37-cp37m-manylinux1_i686.whl
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Release files / stria-0.1.3-cp37-cp37m-macosx_10_9_x86_64.whl
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Release files / stria-0.1.3-cp36-cp36m-win_amd64.whl
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Release files / stria-0.1.3-cp36-cp36m-win32.whl
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Release files / stria-0.1.3-cp36-cp36m-manylinux2010_x86_64.whl
| Download URL | stria-0.1.3-cp36-cp36m-manylinux2010_x86_64.whl |
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Release files / stria-0.1.3-cp36-cp36m-manylinux2010_i686.whl
| Download URL | stria-0.1.3-cp36-cp36m-manylinux2010_i686.whl |
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Release files / stria-0.1.3-cp36-cp36m-manylinux1_x86_64.whl
| Download URL | stria-0.1.3-cp36-cp36m-manylinux1_x86_64.whl |
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Release files / stria-0.1.3-cp36-cp36m-manylinux1_i686.whl
| Download URL | stria-0.1.3-cp36-cp36m-manylinux1_i686.whl |
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Release files / stria-0.1.3-cp36-cp36m-macosx_10_9_x86_64.whl
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Release files / stria-0.1.3-cp35-cp35m-win_amd64.whl
| Download URL | stria-0.1.3-cp35-cp35m-win_amd64.whl |
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Release files / stria-0.1.3-cp35-cp35m-win32.whl
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Release files / stria-0.1.3-cp35-cp35m-manylinux2010_x86_64.whl
| Download URL | stria-0.1.3-cp35-cp35m-manylinux2010_x86_64.whl |
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Release files / stria-0.1.3-cp35-cp35m-manylinux2010_i686.whl
| Download URL | stria-0.1.3-cp35-cp35m-manylinux2010_i686.whl |
|---|---|
| Size | 54.3 kB |
| Tags | CPython 3.5 CPython 3.5 pymalloc Linux glibc 2.12+ x86-32 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/4.3.1 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.0 CPython/3.9.5
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Release files / stria-0.1.3-cp35-cp35m-manylinux1_x86_64.whl
| Download URL | stria-0.1.3-cp35-cp35m-manylinux1_x86_64.whl |
|---|---|
| Size | 56.9 kB |
| Tags | CPython 3.5 CPython 3.5 pymalloc Linux glibc 2.5+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/4.3.1 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.0 CPython/3.9.5
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Release files / stria-0.1.3-cp35-cp35m-manylinux1_i686.whl
| Download URL | stria-0.1.3-cp35-cp35m-manylinux1_i686.whl |
|---|---|
| Size | 54.3 kB |
| Tags | CPython 3.5 CPython 3.5 pymalloc Linux glibc 2.5+ x86-32 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/4.3.1 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.0 CPython/3.9.5
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Release files / stria-0.1.3-cp35-cp35m-macosx_10_9_x86_64.whl
| Download URL | stria-0.1.3-cp35-cp35m-macosx_10_9_x86_64.whl |
|---|---|
| Size | 17.7 kB |
| Tags | CPython 3.5 CPython 3.5 pymalloc macOS 10.9+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/4.3.1 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.0 CPython/3.9.5
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