ENCODE dataframe

I wanted a better way of exploring and downloading raw data from the ENCODE project.

For example, I'd like to get the BAM files for all ChIP-seq experiments done in uninduced MEL cells (from the mm9 assembly).

One strategy would be to individually go through each track hub (e.g., histone mods from LICR, http://genome.cit.nih.gov/cgi-bin/hgFileUi?db=mm9&g=wgEncodeLicrHistone), filter data, and download files individually.

Another strategy would be to go directly to the download page (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/) and extract the files that end in .bam.

This small package takes advantage of the files.txt files (here's an example) that describe all the metadata on the download page.

The files.txt files are downloaded from each ENCODE track hub in the assembly of interest. Then these files are parsed and concatenated together into one big pandas.DataFrame that can be used to find the data you care about.

Installation

pip install encode-dataframe

Usage

Mirror the files. This may take a minute or so. If you've cloned the git repo, you already have a copy of the mm9 files.

>>> import encode_dataframe as edf
>>> edf.mirror_metadata_files('mm9')

Create a large DataFrame:

>>> df = edf.encode_dataframe('mm9')

>>> len(df)
5865

Armed with the dataframe, we can now slice and dice to get the data we care about. Eventually I'd like to run a ChromHMM segmentation on MEL cells, but I need to get the data first . . .

Choose a cell type

>>> interesting = df.cell == 'MEL'

And only BAM files

>>> interesting &= df.type == 'bam'

And only ChIP- or DNase-seq

>>> interesting &= df.dataType.isin(['ChipSeq', 'DnaseSeq'])

And only untreated (in this case, uninduced) cells:

>>> interesting &= df.treatment != 'DMSO_2.0pct'

And only one replicate (some have 2 or 3)

>>> interesting &= df.replicate == '1'

And only those that don't have some issue with them (looks like older versions have some text in the objStatus field):

>>> interesting &= df.objStatus.isnull()

How many do we have to work with?

>>> m = df[interesting]
>>> len(m)
60

Some of these are controls (input or IgG), and there are some duplicates (looks like H3K4me3 ChIP-seq uses 2 different controls; CTCF was done by different groups). How many unique antibodies?

>>> len(m.antibody.unique())
46

So here are the files I should download:

>>> urls = m.url.values