Commit cff94bb8 authored by aknecht2's avatar aknecht2
Browse files

Updated documentation for db. Moved metadata scripts to install.

parent bec441e3
......@@ -321,6 +321,7 @@ class MongoDB(object):
:type accession: string
:param file_type: The file type of the target sample.
:type file_type: string
:returns: A tuple (valid, msg, data)
Gets the associated sample based on accession number and file_type.
For loading input files for workflows the file_type should be fastq
......@@ -357,6 +358,7 @@ class MongoDB(object):
:type experiment_accession: str
:param file_type: File type of samples to grab usually fastq or bam
:type file_type: str
:returns: A tuple (valid, msg, data)
Validates and gets samples for the given experiment. Experiments must
have control and signal samples of the provided file_type to be
......
MongoDB
==============
The MongoDB class is used to manage all interactions with the encode data.
The encode data is available from their website, and can be queried as json
files using the following link:
https://www.encodeproject.org/experiments/?format=json&limit=all
From the list of experiments, we can extract all information for a particular
experiment by requesting a url using the experiment accession:
https://www.encodeproject.org/experiments/ENCSR000AHW/?format=json
Each of these json files is used to load data into mongodb. There is an
enormous amount of metadata for each experiment that follows roughly the
same format. I recommend looking at some experiments to familiarize yourself
with the experiment metadata. For more information about how to create the
mongodb database look at the :ref:`chip-meta-download` and
:ref:`chip-meta-import` scripts.
MongoDB Class
^^^^^^^^^^^^^^
......
......@@ -7,3 +7,9 @@ chip-gen
chip-create-run
^^^^^^^^^^^^^^^
chip-meta-download
^^^^^^^^^^^^^^^^^^^
chip-meta-import
^^^^^^^^^^^^^^^^^
......@@ -10,6 +10,8 @@ setup(
},
scripts = [
"scripts/chip-gen",
"scripts/chip-create-run"
"scripts/chip-create-run",
"scripts/chip-meta-download",
"scripts/chip-meta-import"
]
)
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