Sequence Extraction

Extract sequences based on the sequence ID. 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 extract_sequences():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    output_dir = 'tests/output'
    extract = pysegul.SequenceExtraction(
        input_format,
        datatype,
        output_dir,
        output_format,
        )
    extract.input_dir = input_dir
    # Using regular expression method
    extract.extract_regex("(?i)^(abce)")
    # using list of sequence ID method
    extract.extract_list(['abce1', 'abce2'])

You can also input the alignment paths in a list directly instead of using a directory. Replace the input_dir with input_files and provide a list of paths. Then, call the from_files method instead of from_dir.

import pysegul

def extract_sequences():
    input_path = ['tests/align-data/alignment1.nex', 'tests/align-data/alignment2.nex']
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    output_dir = 'tests/output'
    extract = pysegul.SequenceExtraction(
        input_format,
        datatype,
        output_dir,
        output_format,
        )
    extract.input_files = input_path
    # Using regular expression method
    extract.extract_regex("(?i)^(abce)")
    # using list of sequence ID method
    extract.extract_list(['abce1', 'abce2'])