Numpy import error #1
Description
Hi All,
I am trying to extract features from a given fasta file (DNA or RNA), using kmer.py script as per the description in the README. While running the code in a juypter notebook it is throwing the following error.
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-11-1066287f4a62> in <module>
4
5 k = 6 # choose the value for k
----> 6 obj = kmer_featurization(k)
7 kmer_features = obj.obtain_kmer_feature_for_a_list_of_sequences(seq_list, write_number_of_occurrences=False)
~/Documents/lncRNAs_project_2020/scripts_2021/kmer/kmer.py in __init__(self, k)
8 """
9 self.k = k
---> 10 self.letters = ['A', 'T', 'C', 'G']
11 self.multiplyBy = 4 ** np.arange(k-1, -1, -1) # the multiplying number for each digit position in the k-number system
12 self.n = 4**k # number of possible k-mers
NameError: name 'np' is not defined
I am running the script in python 3.2.7, and I have numpy installed.
This is how I tried running the script,
from kmer import kmer_featurization
import numpy as np
seq_list = ['ATCGA', 'TCGAC'] # a list of DNA sequences
k = 6 # choose the value for k
obj = kmer_featurization(k)
kmer_features = obj.obtain_kmer_feature_for_a_list_of_sequences(seq_list, write_number_of_occurrences=False)
Any suggestions/help is much appreciated!