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I want to update the numbers in idx field if there is any matching letter between the vals from two consecutive row.

Input data = '''postidxtvals
 23t4tabc
 25t7tatg
 29t8tctb
 35t1txyz
 37t2tmno
 39t3tpqr
 41t6trtu
 45t5tlfg'''

Explantion: Since there is letteramatching between idx 4 and 7 the idx at pos 25 will be updated to 4, but again there istmatching between vals at pos 25 and 29 we update the idx at 29 also to 4 instead of just 7.

#Expected output to a file (tab separated):
pos idx vals
23 4 abc
25 4 atg
29 4 ctb
35 1 xyz
37 2 mno
39 3 pqr
41 3 rtu
45 5 lfg

I have written the given workable code (below) so far, and would also like to

• write the expected output to a file


• optimize the code for the work I am doing.


• the answer has to follow my method of reading two consecutive rows (as keys, values) pairs at a time in ordered way. The reason is this question is just a trial of other problem I am trying to solve. Other parts of the code can be optimized in any pythonic way.

Code:

import csv
import itertools
import collections
import io
from itertools import islice

data = '''postidxtvals
23t4tabc
25t7tatg
29t8tctb
35t1txyz
37t2tmno
39t3tpqr
41t6trtu
45t5tlfg'''


data_As_Dict = csv.DictReader(io.StringIO(data), delimiter='t')
grouped = itertools.groupby(data_As_Dict, key=lambda x: x['idx'])

''' Function to read the data as key, val pairs in Ordered way.'''
def accumulate(data):
 acc = collections.OrderedDict()
 for d in data:
 for k, v in d.items():
 acc.setdefault(k, ).append(v)
 return acc


''' Store data as keys,values '''
grouped_data = collections.OrderedDict()
for k, g in grouped:
 grouped_data[k] = accumulate(g)


''' Print the very first k1. After this we only need to print k2 and update the idx '''
header_with_1stK1 = io.StringIO(data).read().split('n')[0:2]
print('n'.join(header_with_1stK1))

''' make an empty new_k2 value. This k2 value is updated and carried on base on match between vals from two different rows. '''
k2_new = ''

for n in range(2):
 if n > 0:
 break. # just to run the loop one time and to prevent resetting of k2_new values to ‘’

 ''' Now, read as keys, values pairs for two consecutive keys '''
 for (k1, v1), (k2, v2) in zip(grouped_data.items(), islice(grouped_data.items(), 1, None)):

 v1_vals = ''.join(v1['vals'])
 v2_vals = ''.join(v2['vals'])

 v1_list = list(v1_vals)
 v2_list = list(v2_vals)

 ''' to check if there is any matching element '''
 commons = [x for x in v1_list if x in v2_list]

 v2_pos = ''.join(v2['pos'])


 ''' start updating the idx values '''
 if k2_new == '':
 if len(commons) > 0:
 k2_new = k1
 print('t'.join([v2_pos, k2_new, v2_vals]))

 else:
 k2_new = ''
 print('t'.join([v2_pos, k2, v2_vals]))


 elif k2_new != '':
 if len(commons) > 0:
 k2_new = k2_new
 print('t'.join([v2_pos, k2_new, v2_vals]))

 else:
 k2_new = ''
 print('t'.join([v2_pos, k2, v2_vals]))


print('nUpdated the idx values')

I may contribute by first eliminating the itertools and collections module.

import csv
import io

Set the data

 data = '''postidxtvals
 23t4tabc
 25t7tatg
 29t8tctb
 35t1txyz
 37t2tmno
 39t3tpqr
 41t6trtu
 45t5tlfg''';
print('INPUT:n'+data);

Create a "set" of OrderedDictionary object based on the data, and then save it as a list. This is because data_As_dict is not subscriptable, relatively not flexible for work in iteration, and each dictionary in it will be erased after being reused.

data_As_Dict = csv.DictReader(io.StringIO(data), delimiter='t');
list_Of_Dict = [i for i in data_As_Dict];

Now it is saved as a list, we can access each row. We can check the condition by simply checking v1+v2. For example, if v1='abc' and v2='atg', then v1+v2='abcatg'. We have a pattern, 'a' occurs twice, and the others are unique. So here is your condition : len(set(v1+v2)) != len(v1+v2)

Here is the code for creating the output,

for i in range(0, len(list_Of_Dict)-1):
 v1 = list_Of_Dict[i]['vals'];
 v2 = list_Of_Dict[i+1]['vals'];
 if len(set(v1+v2)) != len(v1+v2):
 list_Of_Dict[i+1]['idx'] = list_Of_Dict[i]['idx'];


output_data = 'postidxtvalsn';
for i in list_Of_Dict:
 output_data += i['pos']+'t'+i['idx']+'t'+i['vals']+'n';
print('OUTPUT:n'+output_data);

Full code:

import csv
import io

data = '''postidxtvals
23t4tabc
25t7tatg
29t8tctb
35t1txyz
37t2tmno
39t3tpqr
41t6trtu
45t5tlfg''';

print('INPUT:n'+data);
data_As_Dict = csv.DictReader(io.StringIO(data), delimiter='t');

list_Of_Dict = [i for i in data_As_Dict];

for i in range(0, len(list_Of_Dict)-1):
 v1 = list_Of_Dict[i]['vals'];
 v2 = list_Of_Dict[i+1]['vals'];
 if len(set(v1+v2)) != len(v1+v2):
 list_Of_Dict[i+1]['idx'] = list_Of_Dict[i]['idx'];


output_data = 'postidxtvalsn';
for i in list_Of_Dict:
 output_data += i['pos']+'t'+i['idx']+'t'+i['vals']+'n';
print('OUTPUT:n'+output_data);