Quick Start¶
Installation¶
sra2mongo Usage¶
sra2mongo
is the command line tool provided by sramongo. To get a full set of
options run sra2mongo -h
. A simple query would look like:
sra2mongo \
--email john.smith@example.com \
--query '"Drosophila melanogaster"[orgn]'
The \
allows for breaking the command on multiple lines. This command will
query the SRA for "Drosophila melanogaster"[orgn]
, download the XML for all
of the runs, and parse the XML into a database named ‘sramongo’.
A (see sramongo mappings) for a list of database fields.
Note
The query string is passed directly to SRA, so any query options such as [orgn], [pid], or [author] will work. Also queries can include boolean operators (i.e., AND, OR).
Querying the Database¶
Todo
Add section about querying the database using mongoengine and pymongo. Until then follow mongoengines docs