[Biopython-dev] Tutorial

Tiago Antao tra at popgen.net
Sun Dec 13 20:17:42 UTC 2015


On 2015-12-13 06:03, Peter Cock wrote:
> If you spotted any untested example without dependencies,
> please try adding the doctest comment markup to see if we
> can expand the test_Tutorial.py coverage.

As I go through the problems with the notebook, I can report the issues 
on github, but I am diverting all the time that I have to do this to the 
notebook version.

> What other big datasets are you thinking of here? That was
> all that came to mind, but the Tutorial has a lot in it.

I will report this as I go through the tutorial conversion, but for now:

1. As you say, the uniprot file

2. This code on the same chapter:
#this will download the files - Currently there are more than 16, but we 
will do only 4
import os
for i in range(1, 5):
     os.system('wget ftp://ftp.ncbi.nih.gov/genbank/gbvrl%i.seq.gz -O 
data/gbvrl%i.seq.gz' % (i, i))
     os.system('gzip -d data/gbvrl%i.seq.gz' % i)

Currently, the latex tutorial will download 16 files. These are not 
complete the whole current database, and lookup code afterwards will 
fail (i.e. there is a bug in the tutorial).

I opted to download only 4 files (as per above) and to make sure that I 
get a very early key example.


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