Sequence Addition

Add sequences to existing sequence files. Input sequences are matched to destination files by file name, excluding the extension. The input and destination files can be in different formats. The output is unaligned: gaps and missing data are removed. The output format can be fasta or fasta-int.

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 add_sequences():
    input_dir = 'tests/new-sequences'
    input_format = 'fasta'
    datatype = 'dna'
    output_dir = 'tests/output'
    add = pysegul.SequenceAddition(
        input_format,
        datatype,
        output_dir,
        # Optional. Default: 'fasta'
        output_fmt='fasta',
        # Optional. Write only the destination files that received new sequences.
        added_only=False,
        )
    add.input_dir = input_dir
    # Or use a list of files:
    # add.input_files = ['tests/new-sequences/locus1.fas']

    # Add to all files in a destination directory
    add.add_to_dir('tests/align-data', 'nexus')
    # Or add to a list of destination files
    # add.add_to_files(['tests/align-data/locus1.nex'], 'nexus')

To add all input sequences into a single file:

# Set include_filename to True to append the input file name to each sequence ID.
add.add_to_file('tests/output/all_sequences.fas', include_filename=True)