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I am a beginner in Python (I am a biologist) and I have a file with the results from a particular software and i would like to parse the result using python. From the following output I would like to get just the score and would like to split the sequence into individual amino acids.

no. score Sequence

1   0.273778    FFHH-YYFLHRRRKKCCNNN-CCCK---HQQ---HHKKHV-FGGGE-EDDEDEEEEEEEE-EE--
2   0.394647    IIVVIVVVVIVVVVVVVVVV-CCCVA-IVVI--LIIIIIIIIYYYA-AVVVVVVVAAAAV-AST-
3   0.456667        FIVVIVVVVIXXXXIGGGGT-CCCCAV -------------IVBBB-AAAAAA--------AAAA-  
4   0.407581    MMLMILLLLMVVAIILLIII-LLLIVLLAVVVVVAAAVAAVAIIII-ILIIIIIILVIMKKMLA-
5   0.331761    AANSRQSNAAQRRQCSNNNR-RALERGGMFFRRKQNNQKQKKHHHY-FYFYYSNNWWFFFFFFR-
6   0.452381    EEEEDEEEEEEEEEEEEEEE-EEEEESSTSTTTAEEEEEEEEEEEE-EEEEEEEEEEEEEEEEE-
7   0.460385    LLLLLLLLMMIIILLLIIII-IIILLVILMMEEFLLLLILIVLLLM-LLLLLLLLLLVILLLVL-
8   0.438680    ILILLVVVVILVVVLQLLMM-QKQLIVVLLVIIMLLLLMLLSIIIS-SMMMILFFLLILIIVVL-
9   0.393291    QQQDEEEQAAEEEDEKGSSD-QQEQDDQDEEAAAHQLESSATVVQR-QQQQQVVYTHSTVTTTE-

From the above table,I would like to get a table with the same number,score but the sequences separated individually (columnwise) so it should look like 

no.      score         amino acid(1st column)

1      0.273778         F

2      0.395657         I

3      0.456667         F

another table representing the second column of amino acids

no       score       amino acid (2nd column)

1       0.273778         F

2       0.395657         I

3       0.456667         I

third table representing the third column of amino acids and fourth table for 4th column of amino acids and so on

Thanks in advance for the help

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  • 3
    What do the F, I and f stand for? Are these the first characters from the strings above? Why the f in the third line and not F? We are not beginners in Python, but we are no biologists either. We can help you with Python but you have to explain what are the individual amino acids here. Commented Dec 12, 2011 at 11:48
  • it is supposed to be F...i have edited the question.(F,I;F)are amino acid codes,this is a result of a sequence alignment.I would like to split the entire sequnece columnwise with the the score and serial no. Commented Dec 12, 2011 at 11:51
  • Your description how to get to the letters is still not entirely clear. Maybe it would be good to add some examples with sequences and how to get the desired result. Commented Dec 12, 2011 at 11:55
  • Thanks a lot for all the answers. Commented Dec 14, 2011 at 10:51

4 Answers 4

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5

Assuming you've opened the file containing this data as f, then your example can be reproduced with:

for ln in f:    # loop over all lines
    seqno, score, seq = ln.split()
    print("%s    %s    %s" % (seqno, score, seq[0]))

To split out the sequence, you need to additionally loop over the letters in seq:

for ln in f:
    seqno, score, seq = ln.split()
    for x in seq:
        print("%s    %s    %s" % (seqno, score, seq[0]))

This will print the sequence number and score lots of times. I'm not sure if that's what you want.

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2 Comments

And if you plan on doing anything further with the sequence, I recommend converting it to a Biopython (www.biopython.org) Sequence object.
Thanks for the suggestions,i would like to just split the sequence,i have edited the question accordingly.
0

From your example I guess that:

  • you want to save each table to a different results file.
  • each sequence is 65 characters long
  • some sequences contains meaningless white-spaces which has to be removed (line 3 in your example)

Here is my code sample, it reads data from input.dat and writes results to result-column-<number>.dat:

import re
import sys

# I will write each table to different results-file.
# dictionary to map columns (numbers) to opened file objects:
resultfiles = {}


def get_result_file(column):
    # helper to easily access results file.
    if column not in resultfiles:
        resultfiles[column] = open('result-column-%d.dat' % column, 'w')
    return resultfiles[column]


# iterate over data:
for line in open('input.dat'):
    try:
        # str.split(separator, maxsplit)
        # with `maxsplit`=2 it is more fail-proof:
        no, score, seq = line.split(None, 2)

        # from your example I guess that white-spaces in sequence are meaningless,
        # however in your example one sequence contains white-space, so I remove it:
        seq = re.sub('\s+', '', seq)

        # data validation will help to spot problems early:
        assert int(no), no          
        assert float(score), score
        assert len(seq) == 65, seq

    except Exception, e:
        # print the error and continue to process data:
        print >> sys.stderr, 'Error %s in line: %s.' % (e, line)
        continue  # jump to next iteration of for loop.

    # int(), float() will rise ValueError if no or score aren't numbers
    # assert <condition> will rise AssertionError if condition is False.

    # iterate over each character in amino sequance:
    for column, char in enumerate(seq, 1):
        f = get_result_file(column)
        f.write('%s    %s    %s\n' % (no, score, char))


# close all opened result files:
for f in resultfiles.values():
    f.close()

Notable functions used in this example:

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7 Comments

Thanks for the help,i get an error in line 26.assert int(no), no ValueError: invalid literal for int() with base 10: '#column'
Can you find a line in your data file which contains text "#column"? Could you show me that line by editing your question? From the data-sample which you provided in question this error cannot rise.
the data i provided is just an example,and also i want the '-' in my data as well as they mean something.i do not know how i can upload my entire result file,may be it can help,sorry for not being able to explain properly..
You do not need to attach entire file, but your sample has to display all possible variations of data. Find a line which looks different and add that line to your data-sample. You told that my script fails on line which starts with '#column'. Could it be that # indicates a comment and should be skipped?
i just uploaded the file,so when i split i want also the hyphen '-'to be included as it means something in my data so i want the number ,score and the sequence split into individual columns...
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I don't think it's useful to create tables.
Just put the data in an adapted structure and use a function that displays what you need at the moment you need:

with open('bio.txt') as f:
    data = [line.rstrip().split(None,2) for line in f if line.strip()]


def display(data,nth,pat='%-6s  %-15s  %s',uz=('th','st','nd','rd')):
    print pat % ('no.','score',
                 'amino acid(%d%s column)' %(nth,uz[0 if nth//4 else nth]))
    print '\n'.join(pat % (a,b,c[nth-1]) for a,b,c in data)    

display(data,1)
print
display(data,3)
print
display(data,7)

result

no.     score            amino acid(1st column)
1       0.273778         F
2       0.394647         I
3       0.456667         F
4       0.407581         M
5       0.331761         A
6       0.452381         E
7       0.460385         L
8       0.438680         I
9       0.393291         Q

no.     score            amino acid(3rd column)
1       0.273778         H
2       0.394647         V
3       0.456667         V
4       0.407581         L
5       0.331761         N
6       0.452381         E
7       0.460385         L
8       0.438680         I
9       0.393291         Q

no.     score            amino acid(7th column)
1       0.273778         Y
2       0.394647         V
3       0.456667         V
4       0.407581         L
5       0.331761         S
6       0.452381         E
7       0.460385         L
8       0.438680         V
9       0.393291         E
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0

Here is a simple working solution:

#opening file: "db.txt" full path to file if it is in the same directory as python file 
#you can use any extension for the file ,'r' for reading mode
filehandler=open("db.txt",'r') 
#Saving all the lines once in a list every line is a list member
#Another way: you can read it line by line
LinesList=filehandler.readlines()
#creating an empty multi dimension list to store your results
no=[]
Score=[]
AminoAcids=[] # this is a multi-dimensional list for example index 0 has a list of char. of first line and so on
#process each line assuming constant spacing in the input file
#no is the first char. score from char 4 to 12 and Amino from 16 to end
for Line in LinesList:
    #add the no
    no.append(Line[0])
    #add the score
    Score.append(Line[4:12])
    Aminolist=list(Line[16:]) #breaking the amino acid as each character is a list element
    #add Aminolist to the AminoAcids Matrix (multi-dimensional array)
    AminoAcids.append(Aminolist)

#you can now play with the data!
#printing Tables ,you can also write them into a file instead
for k in range(0,65):
    print"Table %d" %(k+1) # adding 1 to not be zero indexed
    print"no. Score      amino acid(column %d)" %(k+1)
    for i in range(len(no)):
        print "%s   %s   %s" %(no[i],Score[i],AminoAcids[i][k])

Here is a part of result appears on the console:

Table 1
no. Score      amino acid(column 1)
1   0.273778   F
2   0.394647   I
3   0.456667   F
4   0.407581   M
5   0.331761   A
6   0.452381   E
7   0.460385   L
8   0.438680   I
9   0.393291   Q
Table 2
no. Score      amino acid(column 2)
1   0.273778   F
2   0.394647   I
3   0.456667   I
4   0.407581   M
5   0.331761   A
6   0.452381   E
7   0.460385   L
8   0.438680   L
9   0.393291   Q
Table 3
no. Score      amino acid(column 3)
1   0.273778   H
2   0.394647   V
3   0.456667   V
4   0.407581   L
5   0.331761   N
6   0.452381   E
7   0.460385   L
8   0.438680   I
9   0.393291   Q
Table 4
no. Score      amino acid(column 4)
1   0.273778   H
2   0.394647   V
3   0.456667   V
4   0.407581   M
5   0.331761   S
6   0.452381   E
7   0.460385   L
8   0.438680   L
9   0.393291   D
Table 5
no. Score      amino acid(column 5)
1   0.273778   -
2   0.394647   I
3   0.456667   I
4   0.407581   I
5   0.331761   R
6   0.452381   D
7   0.460385   L
8   0.438680   L
9   0.393291   E
Table 6
no. Score      amino acid(column 6)
1   0.273778   Y
2   0.394647   V
3   0.456667   V
4   0.407581   L
5   0.331761   Q
6   0.452381   E
7   0.460385   L
8   0.438680   V
9   0.393291   E
Table 7
no. Score      amino acid(column 7)
1   0.273778   Y
2   0.394647   V
3   0.456667   V
4   0.407581   L
5   0.331761   S
6   0.452381   E
7   0.460385   L
8   0.438680   V
9   0.393291   E
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