Sequence ID Extraction & Mapping

Extract unique sequence IDs from a collection of alignments and map them to the corresponding loci.

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_sequence_id():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    # Set map_id to True to map the sequence ID
    # to the corresponding loci
    map_id = False
    prefix = 'concatenated'
    output_dir = 'tests/output'
    concat = pysegul.IDExtraction(
        input_format,
        datatype,
        output_dir,
        map_id,
        prefix
        )
    concat.from_dir(input_dir)

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_sequence_id():
    input_path = ['tests/align-data/alignment1.nex', 'tests/align-data/alignment2.nex']
    input_format = 'nexus'
    datatype = 'dna'
    map_id = False
    prefix = 'concatenated'
    output_dir = 'tests/output'
    concat = pysegul.IDExtraction(
        input_format,
        datatype,
        output_dir,
        map_id,
        prefix
        )
    concat.from_files(input_path)