API Usage

Using the Python API

After installation of blast2galaxy the Python API can be imported into your Python application via import blast2galaxy.

Note

If using the API the BLAST+ or DIAMOND results are not written to a file but instead are returned from the called API function.

You can then perform BLAST or DIAMOND requests using the configured default profile like so:

result = blast2galaxy.blastn(
    query = 'dna_sequence.fasta',
    db = 'database_id',
    outfmt = '6'
)

A specific profile can be used like so:

result = blast2galaxy.blastp(
    profile = 'blastp',
    query = 'protein_sequence.fasta',
    db = 'database_id',
    outfmt = '6'
)

Instead of a filename it is also possible to provide the query as a Python string. This is helpful in the situation of an integration with other tools / databases where writing intermediate files for query sequences is not desired.

protein_seq = """
>sp|P62805|H4_HUMAN Histone H4 OS=Homo sapiens OX=9606 GN=H4C1 PE=1 SV=2
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
"""

result = blast2galaxy.blastp(
    profile = 'blastp',
    query_str = protein_seq,
    db = 'database_id',
    outfmt = '6'
)

Tip

You can find all possible arguments and parameters in the API reference.

Exceptions

blast2galaxy throws the following exceptions when used in API mode:

blast2galaxy.errors.Blast2galaxyConfigFileError

Bases: Blast2galaxyError

Raised for an error with the configuration of blast2galaxy

blast2galaxy.errors.Blast2galaxyError

Bases: Exception

Base class for all exceptions raised by blast2galaxy, used for general errors