File operation examples

This page shows how to read a dataset using the fileOperation module of the EnrichRBP

from EnrichRBP.filesOperation import read_fasta_file, read_label

Load the sequences

Function read_fasta_file reads a .txt, .fasta or .fa text file according to the path given in the parameters, and filters or replaces empty lines and ‘T’ characters, finally it returns a numpy array containing all sequences.

fasta_path = '/home/wangyansong/wangyubo/EnrichRBP/src/RNA_datasets/circRNAdataset/AGO1/seq' # Replace the path to load your own sequences of dataset

sequences = read_fasta_file(fasta_path)
print(type(sequences))
print(sequences.shape)

output:

<class 'numpy.ndarray'>
(34636,)

Load the labels

Function read_label reads a text file and returns a numpy array containing labels corresponding to the sequences.

label_path = '/home/wangyansong/wangyubo/EnrichRBP/src/RNA_datasets/circRNAdataset/AGO1/label' # Replace the path to load your own labels of dataset

label = read_label(label_path)
print(type(label))
print(label.shape)

output:

<class 'numpy.ndarray'>
(34636,)