Question

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

Answer 1

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:

• enumerate
• str.split
• re.sub