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Parsing-Theory-II.md

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Parsing data records II

In many cases you will need to compare data from different files

SwissProt-Human.fasta
>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY
LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
AGEGEN
>sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW
RIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVF
YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF
YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE
EQNKEALQDVEDENQ
>sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH
MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSW
RVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESK
VFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFS
VFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDE
EAGEGN
...
...
...

Check the file cancer-expressed.txt

Q5XXA6
Q9Y5P2
Q14667
O75387
Q8WV07
Q8CH62
Q9GZY1
Q9NQQ7
Q8VCX2
Q7Z769

First, you have to store the 10 Uniprot ID in a data structure

  • Read 10 SwissProt ACs from a file
  • Store them into a data structure

Lists are nice and veeeeery flexible data structures

['Q5XXA6', 'Q9Y5P2', 'Q14667', 'O75387', 'Q8WV07','Q8CH62', 'Q9GZY1', 'Q9NQQ7', 'Q8VCX2', 'Q7Z769']

List data structure

A list is a mutable ordered collection of objects

The elements of a list can be any kind of object:

  • numbers
  • strings
  • tuples
  • lists
  • dictionaries
  • function calls
  • etcetera
L = [1, [2,3], 4.52, 'DNA']

L = []  # the empty list

Operations with lists

slot

>>> L = [1,"hello",12.1,[1,2,"three"],"seq",(1,2)]
>>> L[0]  # indexing
1
>>> L[3]  # indexing
[1, 2, 'three']
>>> L[3][2]  # indexing
'three'
>>> L[-1]  # negative indexing
(1, 2)
>>> L[2:4]
[12.1, [1, 2, 'three']]  # slicing
>>> L[2:]
[12.1, [1, 2, 'three'], 'seq', (1, 2)] #slicing shorthand
>>>

The elements of a list can be changed/replaced after the list has been defined These operations CHANGE the list
l[i] = x
l[i:j] = t
del l[i:j]
del l[i:j:k]
l.append(x)
l.extend(s)

s = any sequence

>>> l = [2,3,5,7,8,['a','b'],'a','b','cde']
>>> l[0] = 1
>>> l
[1, 3, 5, 7, 8, ['a', 'b'], 'a', 'b', 'cde']
>>> l[0:3] = 'DNA'
>>> l
['D', 'N', 'A', 7, 8, ['a', 'b'], 'a', 'b', 'cde']
>>> del l[0:5]
>>> l
[['a', 'b'], 'a', 'b', 'cde']
>>> l.append('DNA')
>>> l
[['a', 'b'], 'a', 'b', 'cde', 'DNA']
>>> l.extend('dna')
>>> l
[['a', 'b'], 'a', 'b', 'cde', 'DNA', 'd', 'n', 'a']
>>>

The elements of a list can be changed/replaced after the list has been defined
l.count(x)
l.index(x)
l.insert(i, x)
l.pop(i)
l.remove(x) 
>>> l = [1,3,5,7,8,['a','b'],'a','b','cde']
>>> l.count('a')
>>> l
1
>>> l.index(8)
4
>>> l.insert(4, 80)
>>> l
[1, 3, 5, 7, 80, 8, ['a', 'b'], 'a', 'b', 'cde']
>>> l.pop(4)
80
>>> l
[1, 3, 5, 7, 8, ['a', 'b'], 'a', 'b', 'cde']
>>> l.pop()
'cde'
>>> l
[1, 3, 5, 7, 8, ['a', 'b'], 'a', 'b']
>>> l.remove(8)
[1, 3, 5, 7, ['a', 'b'], 'a', 'b']
The elements of a list can be changed/replaced after the list has been defined
l.reverse()
l.sort()
sorted(l) 
>>> l = [4, 3, 2, 1, 5, 6, 7, 8]
>>> l.reverse()
>>> l
[8, 7, 6, 5, 1, 2, 3, 4]
>>> new = sorted(l)
>>> new
[1, 2, 3, 4, 5, 6, 7, 8]
>>> l
[8, 7, 6, 5, 1, 2, 3, 4]
>>> l.sort()
>>> l
[1, 2, 3, 4, 5, 6, 7, 8]

Putting together lists and loops

range() and xrange() built-in functions

>>> range(10)
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
>>> range(1, 11)
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
>>> range(0, 30, 5)
[0, 5, 10, 15, 20, 25]
>>> range(0, 10, 3)
[0, 3, 6, 9]
>>> range(0, -10, -1)
[0, -1, -2, -3, -4, -5, -6, -7, -8, -9]
>>> range(0)
[]
>>> range(1, 0)
[]
# the xrange()method is more commonly used in for loops than range()
>>>for i in xrange(5):
…             print i
…
0,1,2,3,4

The xrange() method generates the values upon call, i.e. it does not store them into a variable

Indexing

indexing

Computers treat an address in memory as the starting point of a body of data. In the same sense, an index in Python always refers to such a starting point, something that is in between two objects in memory. We humans in contrast always count the objects themselves.

Challenge #1

  • Read 10 SwissProt ACs from a file
  • Store them into a list
  • Print the list

See the solution to Challenge #1



Challenge #2

  • Create a list containing Uniprot ACs extracted from a FASTA file
  • Print the list

See the solution to Challenge #1



Challenge #3

  • Read the human FASTA file one record after the other. Check if the record header contains one of the 10 ACs.
  • If YES, copy the header to a new file.

See the solution to Challenge #1



Challenge #4

Read a multiple sequence file in FASTA format and write to a new file only the records the Uniprot ACs of which are present in the list created in Program 1

Check the file SwissProt-Human.fasta

>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
>sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ
>sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens
GNYWHAHMGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEEAGEGN

See the solution to Challenge #4

Putting together conditions and loops while loops

The while statement is used for executing a set of statements until a given condition is met

**while <condition 1>:
<statements 1>**

>>> a = 1
>>> while a < 5:
...     print a,
...     a = a + 1

BUT:

>>> a = 1
>>> while a > 0:
...     if a == 5: break
...     print a,
...     a = a + 1
... else: print "loop terminated"
...
1 2 3 4

The Boolean values True and False

if and while statements return a False value when they are applied to:

  • None
  • 0
  • Empty data structures: '',(),[],{}

The statements in an if or a while block are executed only if the condition returns the value True.

>>> p = 'protein'
>>> if p: print 'True'
...
True
>>> n = 0
>>> while 1:
...     print n,
...     n = n + 1
...     if n > 5: break
...
0 1 2 3 4 5
>>>

We can use while loops to read files (but usually we won't do it):

cancer_file = open('cancer-expressed.txt')

cancer_list = []
line = cancer_file.readline()
while line:
  AC = line.strip()
  cancer_list.append(AC)
  line = cancer_file.readline()