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Deleting lines in a text file

A sample of the following text file I have:

> 1 -4.6    -4.6    -7.6
> 
> 2 -1.7    -3.8    -3.1
> 
> 3 -1.6    -1.6    -3.1

the data is separated by tabs in the text file and the first column indicates the position.

I need to iterate over each value in a text file separately from column 0 and find the smallest value.

once the lowest value is found, the value should be written to a new text file along with the name and position of the column. Column 0 is named "position" Column 1 "fifteen", column 2 "sixteen" and column "seventeen"

for example, the lowest value in the above data is "-7.6" and is in column 3, which is labeled "seventeen". Therefore, "7.6", "seventeen" and its position value, which in this case is 1, must be written to a new text file.

Then I need to delete multiple lines from the specified text file.

eg. the lowest value is above "-7.6" and is at position "1" and is in column 3, which is called "seventeen". So I need seventeen lines to be removed from the text file, starting at position 1 and including position 1

so the column that has the lowest value indicates the number of rows to be deleted and the position it is found in indicates the starting point of the deletion

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2 answers


Open this file for reading, another file for writing, and copy any lines that don't match the filter:



readfile = open('somefile', 'r')
writefile = open('otherfile', 'w')

for line in readfile:
  if not somepredicate(line):
    writefile.write(line)

readfile.close()
writefile.close()
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Here's the kick I think you wanted (although your requirements were pretty tough):

def extract_bio_data(input_path, output_path):
    #open the output file and write it headers
    output_file = open(output_path, 'w')
    output_file.write('\t'.join(('position', 'min_value', 'rows_skipped')) + '\n')

    #map column indexes (after popping the row number) to the number of rows to skip
    col_index = { 0: 15, 
                  1: 16, 
                  2: 17 }

    skip_to_position = 0
    for line in open(input_path, 'r'):
        #remove the '> ' from the beginning of the line and strip newline characters off the end
        line = line[2:].strip()

        #if the line contains no data, skip it
        if line == '':
            continue

        #split the columns on whitespace (change this to split('\t') for splitting only on tabs)
        columns = line.split()

        #extract the row number/position of this data
        position = int(columns.pop(0))

        #this is where we skip rows/positions
        if position < skip_to_position:  
            continue

        #if two columns share the minimum value, this will be the first encountered in the list
        min_index = columns.index(min(columns, key=float))

        #this is an integer version of the 'column name' which corresponds to the number of rows that need to be skipped
        rows_to_skip = col_index[min_index]

        #write data to your new file (row number, minimum value, number of rows skipped)
        output_file.write('\t'.join(str(x) for x in (position, columns[min_index], rows_to_skip)) + '\n')

        #set the number of data rows to skip from this position
        skip_to_position = position + rows_to_skip


if __name__ == '__main__':
    in_path = r'c:\temp\test_input.txt'
    out_path = r'c:\temp\test_output.txt'
    extract_bio_data(in_path, out_path)


What was not clear to me:

  • Is there really a ">" at the beginning of each line or is it a copy / paste error?
    • I assumed this was not a bug.
  • Do you want to write "7.6" or "-7.6" to a new file?
    • I assumed you want the original value.
  • Do you want to skip lines in the file? or positions based on the first column?
    • I assumed you want to skip positions.
  • You say you want to remove data from the original file.
    • I assumed that skipping the position is enough.
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