List exercise

In []: 
# 1) pick elements with length > 3 
#     and with first and last letter the same
l = ['', 'xyzzz', 'aabddda', 'xyx', 'bbbb']
In [2]: 
# 2) remove the duplicates in the following list
l = [1,2,2,3,3,5,4,1,1,1]

File stream exercise

Extract taxonomy information from taxonomy file;

Each line contains two fields separated by a tab:

  1. sequence name

  2. taxonomy (including 6 taxon levels separated by ';')

In this exercise, we will count frequncy of domains (first level taxon, "Bacteria in the example bellow)

e.g. Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Da111;

In [7]: 
!wget http://lyorn.idyll.org/~gjr/public2/swc/1k.taxonomy

--2015-01-27 00:43:08--  http://lyorn.idyll.org/~gjr/public2/swc/1k.taxonomy
Resolving lyorn.idyll.org (lyorn.idyll.org)... 35.9.124.246
Connecting to lyorn.idyll.org (lyorn.idyll.org)|35.9.124.246|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 104833 (102K)
Saving to: “1k.taxonomy”


 0% [                                       ] 0           --.-K/s              
100%[======================================>] 104,833     --.-K/s   in 0.06s   

2015-01-27 00:43:08 (1.61 MB/s) - “1k.taxonomy” saved [104833/104833]
In [7]: 
# collect unique
unique_list = []
# collect all
all_list = []
for line in open('1k.taxonomy'):
    # +++add your code+++

# count unique, hint: list.count
# +++add your code+++
In []: