sramongo User Documentation¶
sramongo is a python library and command line tool sra2mongo that queries
NCBI’s sequence read archive(SRA) and
dumps all relevant information into a mongo database. Mongo is a popular document based database, which stores
information as key:value pairs; unlike a typical relational database (e.g.,
SQL) which stores data as rows in multiple related tables. One major advantage
of a document based database to a relation database is that there is no need a
defined schema; attributes can be arbitrarily added or removed and don’t need to
be the same across records. What this means is that you can run sra2mongo to
query and populate your database, then freely modify or add new fields/documents
as part of a processing pipeline.
Roughly speaking sramongo is made up of 3 parts. The first is a parser for SRA XML, the second is an object relational mapper to allow easy interface with mongo, and the third is a command line utility which uses Biopython and Entrez utilities to query the SRA and download the resulting XML.
Warning
Please use this tool responsibly, querying the SRA and dumping large amounts of data can be taxing on their system and may result in blacklisting of your IP address.