November 2018
Intermediate to advanced
360 pages
9h 36m
English
Content preview from Bioinformatics with Python Cookbook - Second Edition
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
Start your free trial
Getting ready
We will download our files in HDF5 format for faster processing. Please be advised that this files are quite big; you will need a good network connection and plenty of disk space:
wget -c ftp://ngs.sanger.ac.uk/production/ag1000g/phase1/AR3/variation/main/hdf5/ag1000g.phase1.ar3.pass.3L.h5wget -c ftp://ngs.sanger.ac.uk/production/ag1000g/phase1/AR3/variation/main/hdf5/ag1000g.phase1.ar3.pass.2L.h5
The files have four crosses with around 20 offspring each. We will use chromosome arms 3L and 2L. At this stage, we also compute Mendelian errors (a subject of the next recipe, so we will delay a detailed discussion until then).
The relevant notebook is Chapter11/Preparation.ipynb. There is also a local sample metadata file in the ...