pysradb 0.1.0

Python package for interacting with SRAdb and downloading datasets from SRA

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pysradb
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.. image:: https://img.shields.io/pypi/v/pysradb.svg
:target: https://pypi.python.org/pypi/pysradb

.. image:: https://travis-ci.com/saketkc/pysradb.svg?branch=master
:target: https://travis-ci.com/saketkc/pysradb



Python package for interacting with SRAdb and downloading datasets from SRA.

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Installation
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Dependecies
===========

.. code-block:: bash

pandas>=0.23.4
tqdm>=4.28
aspera-client
SRAmetadb.sqlite

SRAmetadb
=========

SRAmetadb can be downloaded as:

.. code-block:: bash

wget -c https://starbuck1.s3.amazonaws.com/sradb/SRAmetadb.sqlite.gz && gunzip SRAmetadb.sqlite.gz

aspera-client
=============


`aspera-client` needs to be installed as well. Instructions are available here: https://downloads.asperasoft.com/connect2/
Direct download links:

- Linux: https://download.asperasoft.com/download/sw/connect/3.8.1/ibm-aspera-connect-3.8.1.161274-linux-g2.12-64.tar.gz
- MacOS: https://download.asperasoft.com/download/sw/connect/3.8.1/IBMAsperaConnectInstaller-3.8.1.161274.dmg
- Windows: https://download.asperasoft.com/download/sw/connect/3.8.1/IBMAsperaConnect-ML-3.8.1.161274.msi


Install pysradb
===============
.. code-block:: bash

pip install -U pandas tqdm
git clone https://github.com/saketkc/pysradb.git
cd pysradb
pip install -e .


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Interacting with SRA
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Fetch the metadata table (SRA-runtable)
========================================


.. code-block:: python

from pysradb import SRAdb
db = SRAdb('SRAmetadb.sqlite')
df = db.sra_convert('SRP098789')
df.head()

.. table::

=============== ==================== ====================================================================== ============= ======== ================= ============== ================ ============== ============ ========== ======== ============ ===============
study_accession experiment_accession experiment_title run_accession taxon_id library_selection library_layout library_strategy library_source library_name bases spots adapter_spec avg_read_length
=============== ==================== ====================================================================== ============= ======== ================= ============== ================ ============== ============ ========== ======== ============ ===============
SRP098789 SRX2536403 GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1; Homo sapiens; OTHER SRR5227288 9606 other SINGLE - OTHER TRANSCRIPTOMIC 2104142750 42082855 50
SRP098789 SRX2536404 GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2; Homo sapiens; OTHER SRR5227289 9606 other SINGLE - OTHER TRANSCRIPTOMIC 2082873050 41657461 50
SRP098789 SRX2536405 GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3; Homo sapiens; OTHER SRR5227290 9606 other SINGLE - OTHER TRANSCRIPTOMIC 2023148650 40462973 50
SRP098789 SRX2536406 GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1; Homo sapiens; OTHER SRR5227291 9606 other SINGLE - OTHER TRANSCRIPTOMIC 2057165950 41143319 50
SRP098789 SRX2536407 GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2; Homo sapiens; OTHER SRR5227292 9606 other SINGLE - OTHER TRANSCRIPTOMIC 3027621850 60552437 50
=============== ==================== ====================================================================== ============= ======== ================= ============== ================ ============== ============ ========== ======== ============ ===============

Downloading an entire project arranged experiment wise
======================================================

.. code-block:: python

from pysradb import SRAdb
db = SRAdb('SRAmetadb.sqlite')
df = db.sra_convert('SRP017942')
db.download(df)

Downloading a subset of experiments
===================================

.. code-block:: python

df = db.sra_convert('SRP000941')
db.download(df=df_rna, out_dir='/pysradb_downloads')()

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Demo
****

https://nbviewer.jupyter.org/github/saketkc/pysradb/blob/master/notebooks/demo.ipynb


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Citation
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Pending.

A lot of functionality in `pysradb` is based on ideas from the original `SRAdb package
<https://bioconductor.org/packages/release/bioc/html/SRAdb.html>`_. Please cite the original SRAdb publication:

Zhu, Yuelin, Robert M. Stephens, Paul S. Meltzer, and Sean R. Davis. "SRAdb: query and use public next-generation sequencing data from within R." BMC bioinformatics 14, no. 1 (2013): 19.




* Free software: BSD license
* Documentation: https://saketkc.github.io/pysradb



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History
=======

0.1.0 (12-01-2018)
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* First release on PyPI.