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copied!<p>Here's a stab at what I think you wanted (though your requirements were kind of difficult to follow):</p> <pre><code>def extract_bio_data(input_path, output_path): #open the output file and write it's 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) </code></pre> <p>Things that weren't clear to me:</p> <ol> <li>Is there really "> " at the beginning of each line or is that a copy/paste error? <ul> <li>I assumed it wasn't an error.</li> </ul></li> <li>Did you want "7.6" or "-7.6" written to the new file? <ul> <li>I assumed you wanted the original value.</li> </ul></li> <li>Did you want to skip rows in the file? or positions based on the first column? <ul> <li>I assumed you wanted to skip positions.</li> </ul></li> <li>You say you want to delete data from the original file. <ul> <li>I assumed that skipping positions was sufficient.</li> </ul></li> </ol>

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