biogeek biogeek - 1 year ago 103
Python Question

How to handle index of out range and invalid syntax for a sample with binary values in a list of lists in Pytjon?

The following is my sample that consists of binary values 0 and 1

sample = [['0100','0101','0101''],['011','100','001','001'],['001','001','001']]

For any number of elements in the list and any number of elements in the list of lists I need to do the following:

A. Convert it into a list of lists such that the corresponding elements of each list are strung together in a list of lists

column = [['000','111','000','0111'],['0100','1000','1011'],['000','000','111']

B. Create a counter(nn) to count length of each element and divide by (nn-1)

nn = [[3,3,3,3],[4,4,4],[3,3,3]]
nn - 1 = [[2,2,2,2],[3,3,3,3],[2,2,2]]
d = nn-1
div = nn/d

C. Need to calculate a parameter for pi. Here is a link showing how this can be done for a list

I have tried to write the code for the same. I hit the following errors:

A. l += seq_list[j][i]
IndexError: list index out of range.

I am certain that i,j and k are all in the correct range.

B. counters = [Counter(sub_list) for sub_list in column]
SyntaxError: invalid syntax

Why is it invalid syntax?

Any ideas on how to correct the errors? I tried different ways to do the same, but I am unable to do so.

#Tranposing. Moving along the columns only
column = []
for k in range(len(seq_list)):
for i in range(len(seq_list[k][0])): #Length of the row
l = ""
for j in range(len(seq_list[k])): #Length of the column
l += seq_list[j][i]
print "\n Making the columns as a list: " + str(column)

#Creating a separate list where -/? will not be part of the sequence
tt = ["".join(y for y in x if y in {'0','1'}) for x in column]

#Creating a counter that stores n/n-1 values
counters = [Counter(sub_list) for sub_list in tt]
nn =[]
d = []
for counter in counters:
binary_count = sum((val for key, val in counter.items() if key in "01"))
d = [i - 1 for i in nn]
div = [int(b) / int(m) for b,m in zip(nn, d)]

Answer Source

I think this should work for you:

seq_list = [['0100','0101','0101'],['011','100','001','001'],['001','001','001']]

results = []
for k in range(len(seq_list)):
    column_list = [[] for i in range(len(seq_list[k][0]))]
    for seq in seq_list[k]:
        for i, nuc in enumerate(seq):
    tt = ["".join(y for y in x if y in {'0','1'}) for x in column_list]

### Creating a counter that stores n/n-1 values
BINARY = {'0','1'}
counts = [[sum(c in BASES for c in s) for s in pair] for pair in results]
countsminusone1 = [[(sum(c in BINARY for c in s)-1) for s in pair] for pair in results]
countsminusone = [[1 if x <= 0 else x for x in pair] for pair in countsminusone1]
bananasplit = [[n/d for n, d in zip(subq, subr)] for subq, subr in zip(counts, countsminusone)]
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