write_alignments_to_disk.py

    file_name = 'alignments_' + flavor + '.csv'
    with open(file_name, 'w') as t:
        header = 'b_mz'+ '\t'+ 'b_start'+ '\t'+ 'b_end'+ '\t'+ 'b_ion'+ '\t'+ 'b_charge'+ '\t'+ 'b_pid'+ 'b_score'+ '\t'+ 'y_mz'+ '\t'+ 'y_start'+ '\t'+ 'y_end'+ '\t'+ 'y_ion'+ '\t'+ 'y_charge'+ '\t'+ 'y_pid'+ '\t'+ 'y_score'+ '\n'
        t.write(header)    
    for alignment in alignments:
        b,y= alignment
        b_mass, b_start, b_end, b_ion, b_charge, b_pid, b_score = b
        y_mass, y_start, y_end, y_ion, y_charge, y_pid, y_score = y
        item = str(b_mass)+ '\t' + str(b_start)+ '\t' + str(b_end)+ '\t' + str(b_ion)+ '\t' + str(b_charge) + '\t' + str(b_pid) + '\t' + str(b_score) + str(y_mass)+ '\t' + str(y_start)+ '\t' + str(y_end)+ '\t' + str(y_ion)+ '\t' + str(y_charge) + '\t' + str(y_pid) + '\t' + str(y_score) + '\n'
        with open(file_name, 'a') as t:
            t.write(item)