how to access the individual elements of a matrix in python

**aboxylica** · Jul 8 '07, 06:47 AM

headerList = linelist.pop(0)[1:]
WHAT DOES THIS LINE DO?

Originally posted by bvdet

Check variable 'lineList'. It should look like this:[code=Python]>>> for line in lineList:
... print line
...
['01', '0.00', '3.67', '0.00', '0.00']
['02', '0.00', '0.00', '3.67', '0.00']
['03', '0.00', '0.00', '0.00', '3.67']
['04', '0.00', '3.67', '0.00', '0.00']
['05', '3.67', '0.00', '0.00', '0.00']
['06', '3.46', '0.00', '0.22', '0.00']
['07', '0.00', '0.00', '3.67', '0.00']
['08', '0.00', '0.00', '0.00', '3.67']
['09', '0.00', '0.00', '0.00', '3.67']
['10', '0.00', '3.67', '0.00', '0.00']
['11', '3.67', '0.00', '0.00', '0.00']
['12', '3.67', '0.00', '0.00', '0.00']
['13', '0.00', '0.00', '3.67', '0.00']
['14', '0.00', '0.00', '0.00', '3.67']
['15', '0.00', '0.00', '3.67', '0.00']
['16', '0.00', '3.67', '0.00', '0.00']
>>> [/code]

**bartonc** · Jul 8 '07, 07:06 AM

Originally posted by aboxylica

<snip>what does the strip( ) do?

strip() removes whitespace (or any characters you tell it to) from BOTH ends of a string. Like this:[CODE=python]
>>> s = " had_whitespace "
>>> t = s.strip()
>>> print repr(t) # repr() prints the string representation of a varialbe
'had_whitespace '
>>> [/CODE]

**aboxylica** · Jul 8 '07, 07:22 AM

headerList = linelist.pop(0)[1:]
WHAT DOES THIS LINE DO?

Originally posted by bartonc

strip() removes whitespace (or any characters you tell it to) from BOTH ends of a string. Like this:[CODE=python]
>>> s = " had_whitespace "
>>> t = s.strip()
>>> print repr(t) # repr() prints the string representation of a varialbe
'had_whitespace '
>>> [/CODE]

**bartonc** · Jul 8 '07, 07:27 AM

Originally posted by aboxylica

headerList = linelist.pop(0)[1:]
WHAT DOES THIS LINE DO?

Since I didn't write that, I'll just have to do my best to describe it:
Pop(0) takes the zeroth element from linelist (which looks like another list). The result is stored in an unseen, temporary variable. [1:] takes all but the zeroth element from that temporary variable and that (shortened list) is stored in headerList. You can check it out by doing something like
[CODE=python]temp = linelist.pop(0)
print temp
headerList = temp[1:] # this is called a "slice" from the temp list.
print headerList[/CODE]
Hope that helps.

**aboxylica** · Jul 8 '07, 08:22 AM

thanks for that . but could you give ur mail id..because I am not able to paste my exact file here and am stuck with this problem.plz help!

Originally posted by bartonc

Since I didn't write that, I'll just have to do my best to describe it:
Pop(0) takes the zeroth element from linelist (which looks like another list). The result is stored in an unseen, temporary variable. [1:] takes all but the zeroth element from that temporary variable and that (shortened list) is stored in headerList. You can check it out by doing something like
[CODE=python]temp = linelist.pop(0)
print temp
headerList = temp[1:] # this is called a "slice" from the temp list.
print headerList[/CODE]
Hope that helps.

**bartonc** · Jul 8 '07, 08:43 AM

Originally posted by aboxylica

thanks for that . but could you give ur mail id..because I am not able to paste my exact file here and am stuck with this problem.plz help!

Paste what you can here and I'll format it for you.

**aboxylica** · Jul 8 '07, 08:52 AM

Originally posted by bartonc

Paste what you can here and I'll format it for you.

NA bap
PO A C G T
01 0.00 3.67 0.00 0.00
02 0.00 0.00 3.67 0.00
03 0.00 0.00 0.00 3.67
04 0.00 3.67 0.00 0.00
05 3.67 0.00 0.00 0.00
06 3.46 0.00 0.22 0.00
07 0.00 0.00 3.67 0.00
08 0.00 0.00 0.00 3.67
09 0.00 0.00 0.00 3.67
10 0.00 3.67 0.00 0.00
11 3.67 0.00 0.00 0.00
12 3.67 0.00 0.00 0.00
13 0.00 0.00 3.67 0.00
14 0.00 0.00 0.00 3.67
15 0.00 0.00 3.67 0.00
16 0.00 3.67 0.00 0.00
//
//
NA bcd
PO A C G T
01 42.55 8.75 145.86 8.14
02 0.14 0.53 204.64 0.00
03 126.83 78.02 0.11 0.34
04 0.21 0.17 0.00 204.92
05 0.00 12.38 0.43 192.50
06 174.48 0.95 1.32 28.56
07 79.53 4.70 100.44 20.64
//
//
NA bin
PO A C G T
01 0.45 8.27 0.00 11.39
02 0.00 0.00 10.02 10.09
03 5.80 1.39 0.00 12.93
04 12.33 5.18 2.60 0.00
05 12.43 0.00 0.00 7.68
06 18.55 0.00 1.57 0.00
07 0.05 0.58 0.00 19.48
08 20.11 0.00 0.00 0.00
09 20.06 0.05 0.00 0.00
10 20.11 0.00 0.00 0.00
11 0.00 15.33 0.00 4.78
12 20.06 0.05 0.00 0.00
13 14.99 0.35 4.78 0.00
14 13.64 2.42 3.37 0.68
15 5.03 0.00 15.08 0.00
16 7.23 0.45 10.94 1.49
//
//
I want to add one to each and every element of the file(of course except the first column giving the position)
and want to access the elements like A[01]=,c[02]=,etc..

**bartonc** · Jul 8 '07, 09:50 AM

Originally posted by aboxylica

NA bap
PO A C G T
01 0.00 3.67 0.00 0.00
02 0.00 0.00 3.67 0.00
03 0.00 0.00 0.00 3.67
04 0.00 3.67 0.00 0.00
05 3.67 0.00 0.00 0.00
06 3.46 0.00 0.22 0.00
07 0.00 0.00 3.67 0.00
08 0.00 0.00 0.00 3.67
09 0.00 0.00 0.00 3.67
10 0.00 3.67 0.00 0.00
11 3.67 0.00 0.00 0.00
12 3.67 0.00 0.00 0.00
13 0.00 0.00 3.67 0.00
14 0.00 0.00 0.00 3.67
15 0.00 0.00 3.67 0.00
16 0.00 3.67 0.00 0.00
//
//
NA bcd
PO A C G T
01 42.55 8.75 145.86 8.14
02 0.14 0.53 204.64 0.00
03 126.83 78.02 0.11 0.34
04 0.21 0.17 0.00 204.92
05 0.00 12.38 0.43 192.50
06 174.48 0.95 1.32 28.56
07 79.53 4.70 100.44 20.64
//
//
NA bin
PO A C G T
01 0.45 8.27 0.00 11.39
02 0.00 0.00 10.02 10.09
03 5.80 1.39 0.00 12.93
04 12.33 5.18 2.60 0.00
05 12.43 0.00 0.00 7.68
06 18.55 0.00 1.57 0.00
07 0.05 0.58 0.00 19.48
08 20.11 0.00 0.00 0.00
09 20.06 0.05 0.00 0.00
10 20.11 0.00 0.00 0.00
11 0.00 15.33 0.00 4.78
12 20.06 0.05 0.00 0.00
13 14.99 0.35 4.78 0.00
14 13.64 2.42 3.37 0.68
15 5.03 0.00 15.08 0.00
16 7.23 0.45 10.94 1.49
//
//
I want to add one to each and every element of the file(of course except the first column giving the position)
and want to access the elements like A[01]=,c[02]=,etc..

Lacking your working program pasted here, I'm afraid that the best I can tell you is it should be as simple as:[CODE=python]temp = A[01]
print temp
A[01] = temp + 1
print A[01][/CODE]or even [CODE=python]print A[01]
A[01] += 1
print A[01][/CODE]in a loop through your data structure.

**aboxylica** · Jul 8 '07, 10:07 AM

[CODE=python]
file_=open("hal f1.txt","r")
file_content=fi le_.readlines()
linelist=[line.strip().sp lit() for line in file_content if line != '\n']

headerlist=line list.pop(0)[1:]

keys=[i[0] for i in linelist]

values=[[float(s) for s in item] for item in [j[1:] for j in linelist]]

linedict =dict(zip(keys, values))

datadict={}
for i,item in enumerate(heade rlist):
datadict[item]={}
for key in linedict:
print key
datadict[item][key]=linedict[key][i]
print datadict['A']['01']
[/CODE]

when i execute i get an error that says
keyerror: '01'

<removed quote=bvdet to make this post appear.>

'headerList':[code=Python]>>> headerList
['A', 'C', 'G', 'T']
>>> [/code]The values in 'headerList' will be 'keys' in 'dataDict'. 'dataDict' will be the main dictionary, and the values will be subdictionaries . A dictionary key is associated with a value - in this case the value will be another dictionary. Variable 'keys' contain the subdictionary keys:[code=Python]>>> keys
['01', '02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12', '13', '14', '15', '16']
>>> [/code]'lineDict' is a temporary dictionary created to make it easier to compile the data in the form you wanted:[code=Python]>>> lineDict
{'02': [0.0, 0.0, 3.6699999999999 999, 0.0], '03': [0.0, 0.0, 0.0, 3.6699999999999 999], '13': [0.0, 0.0, 3.6699999999999 999, 0.0], '01': [0.0, 3.6699999999999 999, 0.0, 0.0], '06': [3.46, 0.0, 0.22, 0.0], '07': [0.0, 0.0, 3.6699999999999 999, 0.0], '04': [0.0, 3.6699999999999 999, 0.0, 0.0], '05': [3.6699999999999 999, 0.0, 0.0, 0.0], '08': [0.0, 0.0, 0.0, 3.6699999999999 999], '09': [0.0, 0.0, 0.0, 3.6699999999999 999], '16': [0.0, 3.6699999999999 999, 0.0, 0.0], '12': [3.6699999999999 999, 0.0, 0.0, 0.0], '14': [0.0, 0.0, 0.0, 3.6699999999999 999], '11': [3.6699999999999 999, 0.0, 0.0, 0.0], '15': [0.0, 0.0, 3.6699999999999 999, 0.0], '10': [0.0, 3.6699999999999 999, 0.0, 0.0]}
>>> [/code]Using 'enumerate' on 'headerList', Python gives me these values:[code=Python]>>> for i, item in enumerate(heade rList):
... print i, item
...
0 A
1 C
2 G
3 T
>>> [/code]Here's an interactive example showing what is happening inside the nested for loop:[code=Python]>>> dataDict
{}
>>> key
'10'
>>> item
'T'
>>> lineDict
{'02': [0.0, 0.0, 3.6699999999999 999, 0.0], '03': [0.0, 0.0, 0.0, 3.6699999999999 999], '13': [0.0, 0.0, 3.6699999999999 999, 0.0], '01': [0.0, 3.6699999999999 999, 0.0, 0.0], '06': [3.46, 0.0, 0.22, 0.0], '07': [0.0, 0.0, 3.6699999999999 999, 0.0], '04': [0.0, 3.6699999999999 999, 0.0, 0.0], '05': [3.6699999999999 999, 0.0, 0.0, 0.0], '08': [0.0, 0.0, 0.0, 3.6699999999999 999], '09': [0.0, 0.0, 0.0, 3.6699999999999 999], '16': [0.0, 3.6699999999999 999, 0.0, 0.0], '12': [3.6699999999999 999, 0.0, 0.0, 0.0], '14': [0.0, 0.0, 0.0, 3.6699999999999 999], '11': [3.6699999999999 999, 0.0, 0.0, 0.0], '15': [0.0, 0.0, 3.6699999999999 999, 0.0], '10': [0.0, 3.6699999999999 999, 0.0, 0.0]}
>>> lineDict[key][3]
0.0
>>> dataDict[item] = {}
>>> dataDict[item][key] = lineDict[key][2]
>>> dataDict
{'T': {'10': 0.0}}
>>> [/code]I hope this helps you understand what is happening.

**bartonc** · Jul 8 '07, 10:31 AM

Originally posted by aboxylica

[CODE=python]
file_=open("hal f1.txt","r")
file_content=fi le_.readlines()
linelist=[line.strip().sp lit() for line in file_content if line != '\n']

headerlist=line list.pop(0)[1:]

keys=[i[0] for i in linelist]

values=[[float(s) for s in item] for item in [j[1:] for j in linelist]]

linedict =dict(zip(keys, values))

datadict={}
for i,item in enumerate(heade rlist):
datadict[item]={}
for key in linedict:
print key
datadict[item][key]=linedict[key][i]
print datadict['A']['01']
[/CODE]

when i execute i get an error that says
keyerror: '01'

[CODE=python]
file_=open("hal f1.txt","r")
file_content=fi le_.readlines()
linelist=[line.strip().sp lit() for line in file_content if line != '\n']

headerlist=line list.pop(0)[1:]

keys=[i[0] for i in linelist]

values=[[float(s) for s in item] for item in [j[1:] for j in linelist]]

linedict =dict(zip(keys, values))

# Form the data dictionary first:
datadict={}
for i,item in enumerate(heade rlist):
datadict[item]={}
for key in linedict:
datadict[item][key]=linedict[key][i]

# Then loop through the data structure. But since you have turned
# the data sideways, I can not see the structure at this moment.
[/CODE]

**aboxylica** · Jul 8 '07, 10:32 AM

[CODE=python]file_=open("hal f1.txt","r")
file_content=fi le_.readlines()
linelist=[line.strip().sp lit() for line in file_content if line != '\n']

headerlist=line list.pop(0)[1:]
print headerlist

keys=[i[0] for i in linelist]

values=[[float(s) for s in item] for item in [j[1:] for j in linelist]]

linedict =dict(zip(keys, values))

datadict={}
for i,item in enumerate(heade rlist):
datadict[item]={}
for key in linedict:
print key
datadict[item][key]=linedict[key][i]
print datadict['A']['01'][/CODE]
this is my program. i am getting an error that says
key error:'01' and i do want to add one to all the elements
(i mean the float values)
can you see the error?

**bartonc** · Jul 8 '07, 10:37 AM

Originally posted by aboxylica

[CODE=python]file_=open("hal f1.txt","r")
file_content=fi le_.readlines()
linelist=[line.strip().sp lit() for line in file_content if line != '\n']

headerlist=line list.pop(0)[1:]
print headerlist

keys=[i[0] for i in linelist]

values=[[float(s) for s in item] for item in [j[1:] for j in linelist]]

linedict =dict(zip(keys, values))

datadict={}
for i,item in enumerate(heade rlist):
datadict[item]={}
for key in linedict:
print key
datadict[item][key]=linedict[key][i]
print datadict['A']['01'][/CODE]
this is my program. i am getting an error that says
key error:'01' and i do want to add one to all the elements
(i mean the float values)
can you see the error?

I've answered above.

You must learn to use code tags. Instructions are on the right hand side of the page when you are making your post (or reply). There is also very much helpful information in the How to ask a question section of our Posting Guidelines. Thanks

**bvdet** · Jul 8 '07, 03:53 PM

Originally posted by bartonc

Lacking your working program pasted here, I'm afraid that the best I can tell you is it should be as simple as:[CODE=python]temp = A[01]
print temp
A[01] = temp + 1
print A[01][/CODE]or even [CODE=python]print A[01]
A[01] += 1
print A[01][/CODE]in a loop through your data structure.

It looks like you have three data sets in the file. Which one do you want to work on?

Notice that I simplified my example code by eliminating some of the lines in the data file. It appears that you have not adjusted the code to account for that.

**bvdet** · Jul 8 '07, 03:59 PM

I have modified the first part of my example code to read the first data set in the OP file:[code=Python]fn = r'H:\TEMP\temsy s\data9.txt'
f = open(fn)

line = f.next()
while not line.startswith ('PO'):
line = f.next()

headerList = line.strip().sp lit()[1:]
lineList = []

line = f.next().strip( )
while not line.startswith ('/'):
if line != '':
lineList.append (line.strip().s plit())
line = f.next().strip( )

f.close()[/code]This will add a set amount to every element in the data:[code=Python]# Add 1.0 to every element in dataDict subdictionaries
for keyMain in dataDict:
for keySub in dataDict[keyMain]:
dataDict[keyMain][keySub] += 1.0[/code][code=Python]>>> dataDict
{'A': {'02': 1.0, '03': 1.0, '13': 1.0, '01': 1.0, '06': 4.46, '07': 1.0, '04': 1.0, '05': 4.6699999999999 999, '08': 1.0, '09': 1.0, '10': 1.0, '16': 1.0, '11': 4.6699999999999 999, '15': 1.0, '12': 4.6699999999999 999, '14': 1.0}, 'C': {'02': 1.0, '03': 1.0, '13': 1.0, '01': 4.6699999999999 999, '06': 1.0, '07': 1.0, '04': 4.6699999999999 999, '05': 1.0, '08': 1.0, '09': 1.0, '10': 4.6699999999999 999, '16': 4.6699999999999 999, '11': 1.0, '15': 1.0, '12': 1.0, '14': 1.0}, 'T': {'02': 1.0, '03': 4.6699999999999 999, '13': 1.0, '01': 1.0, '06': 1.0, '07': 1.0, '04': 1.0, '05': 1.0, '08': 4.6699999999999 999, '09': 4.6699999999999 999, '10': 1.0, '16': 1.0, '11': 1.0, '15': 1.0, '12': 1.0, '14': 4.6699999999999 999}, 'G': {'02': 4.6699999999999 999, '03': 1.0, '13': 4.6699999999999 999, '01': 1.0, '06': 1.22, '07': 4.6699999999999 999, '04': 1.0, '05': 1.0, '08': 1.0, '09': 1.0, '10': 1.0, '16': 1.0, '11': 1.0, '15': 4.6699999999999 999, '12': 1.0, '14': 1.0}}
>>> [/code]

**aboxylica** · Jul 9 '07, 06:32 AM

Code:

f=open("weight_matrix.transfac.txt","r")
line=f.next()
while not line.startswith('PO'):
    line=f.next()

headerlist=line.strip().split()[1:]
linelist=[]


line=f.next().strip()
while not line.startswith('/'):
    if line != '':
        linelist.append(line.strip().split())
    line=f.next().strip()
    
keys=[i[0] for i in linelist]
values=[[float(s) for s in item] for item in [j[1:] for j in linelist]]

linedict=dict(zip(keys,values))
datadict={}
for i,item in enumerate(headerlist):
    datadict[item]={}
    for key in linedict:
        datadict[item][key]=linedict[key][i]
        for keymain in datadict:
            for keysub in datadict[keymain]:
                datadict[keymain][keysub]+=1.0
                print datadict

so here is the code that you suggested for creating dictionaries for a file(matrix)
now i have gotta do something like..
supposing the sequence entered is something like "ATATTA".. so A is in the first position so A[01]*T[02]*A[03]*T[04]*T[05]*A[06]=??
the sequence is going to be entered by the user everytime(so it will keep changing)
how do i do this?? what changes should i do??hope I am clear!!
THIS is the file containing the matrix
NA bap
PO A C G T
01 0.00 3.67 0.00 0.00
02 0.00 0.00 3.67 0.00
03 0.00 0.00 0.00 3.67
04 0.00 3.67 0.00 0.00
05 3.67 0.00 0.00 0.00
06 3.46 0.00 0.22 0.00
07 0.00 0.00 3.67 0.00
08 0.00 0.00 0.00 3.67
09 0.00 0.00 0.00 3.67
10 0.00 3.67 0.00 0.00
11 3.67 0.00 0.00 0.00
12 3.67 0.00 0.00 0.00
13 0.00 0.00 3.67 0.00
14 0.00 0.00 0.00 3.67
15 0.00 0.00 3.67 0.00
16 0.00 3.67 0.00 0.00
//
//
NA bcd
PO A C G T
01 42.55 8.75 145.86 8.14
02 0.14 0.53 204.64 0.00
03 126.83 78.02 0.11 0.34
04 0.21 0.17 0.00 204.92
05 0.00 12.38 0.43 192.50
06 174.48 0.95 1.32 28.56
07 79.53 4.70 100.44 20.64
//
//
NA bin
PO A C G T
01 0.45 8.27 0.00 11.39
02 0.00 0.00 10.02 10.09
03 5.80 1.39 0.00 12.93
04 12.33 5.18 2.60 0.00
05 12.43 0.00 0.00 7.68
06 18.55 0.00 1.57 0.00
07 0.05 0.58 0.00 19.48
08 20.11 0.00 0.00 0.00
09 20.06 0.05 0.00 0.00
10 20.11 0.00 0.00 0.00
11 0.00 15.33 0.00 4.78
12 20.06 0.05 0.00 0.00
13 14.99 0.35 4.78 0.00
14 13.64 2.42 3.37 0.68
15 5.03 0.00 15.08 0.00
16 7.23 0.45 10.94 1.49
//
//

how to access the individual elements of a matrix in python

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