GTPB Courses

Data Searching

Searching (and manipulating) your data

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Let’s give a look to the content of the tgac.py available here:

codonAMINO =  {'GCU':'A','GCC':'A','GCA':'A', 'GCG':'A',
'CGU':'R','CGC':'R','CGA':'R','CGG':'R','AGA':'R','AGG':'R',
'UCU':'S','UCC':'S','UCA':'S','UCG':'S','AGU':'S','AGC':'S',
'AUU':'I','AUC':'I','AUA':'I','AUU':'I','AUC':'I','AUA':'I',
'UUA':'L','UUG':'L','CUU':'L','CUC':'L','CUA':'L','CUG':'L',
'GGU':'G','GGC':'G','GGA':'G','GGG':'G','AAU':'N','AAC':'N',
'GUU':'V','GUC':'V','GUA':'V','GUG':'V','GAU':'D','GAC':'D',
'ACU':'T','ACC':'T','ACA':'T','ACG':'T','UGU':'C','UGC':'C',
'CCU':'P','CCC':'P','CCA':'P','CCG':'P','CAA':'Q','CAG':'Q',
'GAA':'E','GAG':'E','CAU':'H','CAC':'H','AAA':'K','AAG':'K',
'UUU':'F','UUC':'F','UAU':'Y','UAC':'Y','AUG':'M','UGG':'W',
'AUG':'START','UAG':'STOP', 'UGA':'STOP', 'UAA':'STOP' }
>>> codonAMINO['GCU']
'A'
>>> codonAMINO['AUG']
’START’
>>> for k in codonAMINO.keys():
...             print k, codonAMINO[k]
GUC V
AUA I
GUA V
GUG V
ACU T
AAC N
etc.


Dictionaries

Dictionaries are unordered collections of objects

Dictionaries are structures for mapping immutable objects (keys) on arbitrary objects (values)

d = {key1:value1, key2:value2, …, keyN:valueN}

lists and dictionaries cannot be used as dictionary keys!!!!

keys must be unique, i.e. the same key cannot be associated to more than one value

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>>> d = {'pep1':'MGSNKSKPKDASQRRRSLEPAENVHGAGG', \
    'pep2':'RSLEPAENVHGAGGGAFPASQTPS'}
>>> len(d)
2

>>> d['pep1']
'MGSNKSKPKDASQRRRSLEPAENVHGAGG'

>>> d['pep3'] = 'ASADGHRGPSAAFAPAAA'
>>> d
{'pep1' : 'MGSNKSKPKDASQRRRSLEPAENVHGAGG',
'pep2' : 'RSLEPAENVHGAGGGAFPASQTPS', 'pep3' :
'ASADGHRGPSAAFAPAAA'}

>>> del d['pep2']
>>> d
{'pep1' : 'MGSNKSKPKDASQRRRSLEPAENVHGAGG',
'pep3' : 'ASADGHRGPSAAFAPAAA'}

>>> d.clear()
>>> d
{ }

>>> dict = {"a":1, "b":2, "c":3}
>>> dict.keys()     #list of dictionary keys
['a', 'c', 'b']

>>> keys = dict.keys()
>>> keys.sort() #sort keys
['a', 'b', 'c']

>>> dict.values() #list of dictionary values
[1, 3, 2]

>>> dict.items() #tuple of dictionary (key,value) pairs
[('a', 1), ('c', 3), ('b', 2)]

>>> dict.has_key("a")   #True if dict has key "a", else False
True

Challenge #1

Using the codonAMINO dictonary from tgac.py available here translate the sequence in rna_seq.fasta. Use a single reading frame.

See the Solution to challenge #1

Challenge #2

Implement program 1 for the three reading frames

See the Solution to challenge #1


Sort values of a dictionary by its keys

# sort values of a dictionary by its keys

structures = {
    '2jel':'antibody',
    '1cse':'subtilisin',
    '1ehz':'tRNA(Phe)',
}

def sort_dict_by_keys(data):
    keys = data.keys()
    keys.sort()
    return [data[k] for k in keys]

print sort_dict_by_keys(structures)


Remove redundancy

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Q5XXA6                                                Q7Z769
Q9Y5P2                                                Q8CH62
Q14667                                                Q9GZY1
O75387                                                Q9NQQ7
Q8WV07                                                Q14667
Q8CH62                                                Q5XXA6
Q9GZY1                                                Q9Y5P2
Q9NQQ7                                                Q14667
Q8VCX2                                                O75387
Q7Z769                                                Q9Y5P2
Q8CH62                                                Q8WV07
Q14667                                                Q8VCX2
Q9NQQ7                                                Q8CH62
Q14667                                                Q14667
Q9Y5P2                                                Q9NQQ7

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Sets

Sets are unordered collections of unique objects they are not sequence-like objects and that they cannot contain identical elements

  • Sets do not support indexing and slicing
  • in and not in operators can be used to test an element for membership in a set.
  • Sets are useful for removing duplicates
  • Set operations: intersection, union, difference, symmetrical difference


Create a new set

In order to create a set, the method set(x) must be used, where x is a sequence-like object (string, tuple, list)

add(x)
update(x)

   
copy() creates a copy
pop(), remove(), discard() remove set elements
pop() deletes a single element randomly
remove(x) removes the element x and returns a message of error if x is not in the set
discard() removes the element x without returning any error message if x is not in the set


S1.union(S2)

The union() between 2 sets S1 and S2 creates a new set with the elements from both S1 and S2.

>>> S1 = set(['a','b','c'])
>>> S2 = set (['c','d','e'])
>>> S1.union(S2)
set(['a', 'c', 'b', 'e', 'd'])
>>> S1 | S2
set(['a', 'c', 'b', 'e', 'd'])


S1.intersection(S2)

The intersection() of 2 sets S1 and S2 creates a new set with the elements common to S1 and S2

>>> S1 = set(['a','b','c'])
>>> S2 = set (['c','d','e'])
>>> S1.intersection(S2)
set(['c'])
>>> S1 & S2
set(['c'])


S1.symmetric_difference(S2)or S1 ^ S2

symmetric_difference() of two sets S1 and S2 creates a new set with elements in either S1 or S2 but not both

>>> S1 = set(['a','b','c'])
>>> S2 = set (['c','d','e'])
>>> S1.symmetric_difference(S2)
set(['a', 'b', 'e', 'd'])
>>> S1 ^ S2
set(['a', 'b', 'e', 'd'])


S1.difference(S2) or S1 - S2

The difference() of two sets S1 and S2 creates a new set with elements in S1 but not in S2

>>> S1 = set(['a','b','c'])
>>> S2 = set (['c','d','e'])
>>> S1.difference(S2)
set(['a', 'b'])
>>> S1 - S2
set(['a', 'b'])
>>> S2 – S1
set(['e', 'd'])


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