Sequence Removal

Remove sequences based on the sequence ID. It is the opposite of sequence extraction. It is faster when the sequence to be removed is less than a half of the total sequences. Available methods:

• Regular expression
• List of sequence ID

Steps

Install PySEGUL using pip if you haven’t done it yet

pip install pysegul

Create a new Python script, import the library, and write python code

import pysegul

def remove_sequences():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    output_dir = 'tests/output'
    remove = pysegul.SequenceRemoval(
        input_format,
        datatype,
        output_dir,
        output_format,
        )
    remove.input_dir = input_dir
    # Using regular expression method
    remove.remove_regex("(?i)^(abce)")
    # using list of sequence ID method
    remove.remove_id_list(['abce1', 'abce2'])