Getting Started¶

Import `omxware` and initialize session¶

import omxware

token = omxware.get_token('omxware_username', 'omxware_pwd')
omx = omxware.omxware(token)

Retrieve genes as a Pandas Dataframe¶

search_string = 'sporulation'
response = omx.genes(gene_name=search_string, page_size=25)

#total_results = response.total_results()
#print(total_results)

results_df = response.results(type='df')
results_df.head()

	Genera	Id	Name	Sequence_length	Type
0	clostridioides	e642254a70da3b1860b03d0755714862	Sporulation kinase A	1995	gene
1	paenibacillus	c22bd7d7ec6d836bfe7ca70caf9c0d56	Sporulation kinase E	1734	gene
2	bacillus	f5f7acff522419f65d867eef0d19376c	Sporulation kinase E	1788	gene
3	bacillus	48d934478603605b8d8540139585f460	Sporulation protein YdcC	1005	gene
4	tindallia	e9b4c151f00d03795645b289bb68e9a7	Sporulation kinase A	2109	gene

Distribution of Genes by Genera¶

response.show_facets(name='genera', topN=7)

_images/output_5_0.png

Retrieve a Gene object as JSON¶

import json

results_json = response.results(type='json')
print(json.dumps(results_json[:3], indent=4, sort_keys=True))

[
    {
        "genera": [
            "clostridioides"
        ],
        "id": "e642254a70da3b1860b03d0755714862",
        "name": "Sporulation kinase A",
        "sequence_length": 1995,
        "type": "gene"
    },
    {
        "genera": [
            "paenibacillus"
        ],
        "id": "c22bd7d7ec6d836bfe7ca70caf9c0d56",
        "name": "Sporulation kinase E",
        "sequence_length": 1734,
        "type": "gene"
    },
    {
        "genera": [
            "bacillus"
        ],
        "id": "f5f7acff522419f65d867eef0d19376c",
        "name": "Sporulation kinase E",
        "sequence_length": 1788,
        "type": "gene"
    }
]

Retrieve Gene data as an Object¶

results_list = response.results(type='list')

# By default, the API returns a `list`
print("Returns: List of {} objects \nResults: {}\n".format(response.type(), response.total_results()) )

gene = results_list[0]
print("Id  \t\t=> " + gene.id())
print("Name   \t\t=> " + gene.name())
print("Sequence   \t=> " + gene.sequence()[:100] + "...")
print("Sequence length => " + str(gene.sequence_length()))

print("\n\n JSON:")
print(gene.json())

Returns: List of gene objects
Results: 73318

Id                  => e642254a70da3b1860b03d0755714862
Name                => Sporulation kinase A
Sequence    => GTGAATAAAAAAAAGATTGTTATTATAGGGATTATTTATTCATTTTTAGTAGTATTTTCACTTACAAATATGTATGTAAATATGGAGTATAATCTAAATG...
Sequence length => 1995


 JSON:
{'id': 'e642254a70da3b1860b03d0755714862', 'name': 'Sporulation kinase A', 'type': 'gene', 'genera': ['clostridioides'], 'sequence_length': 1995}

Retrieve a Gene in FASTA format¶

new_gene_object = omx.genes(ids='00054a98f8ddd95e3f46d9d757137284').results(type='fasta')
print(new_gene_object)

>OMX_gene_00054a98f8ddd95e3f46d9d757137284|Sporulation initiation phosphotransferase F
ATGAACGAGAAGGTGCTGCTGGTTGACGACGACGAGGCCATCCGCGAAGTCCTCAGCCTCTCCATCGCCGACCTGGGCTACGACGTGGAAACCGCCCCCGGCGGCCGCGAAGCCCTGGAGCTGTGCGCCACCTTCAAACCGTCCATCGTGCTCACCGACATCAAGATGCCCGGCATGGACGGCATCGAACTGCTCTCGCGCGTCAAAGCCCTCGATCCCGAGATCGAGGTCATCATGATTTCCGGCCATGGCGACATGGAACTGGCCATCGAGAGCCTCAAGCGCCAGGCCCTGGATTTCCTCACCAAGCCCGTGCGCGACGAACTGCTCACAGCCTCCCTCCACCGGGCCGCCGACCGCGTGTCCATGCGCCGCCAGATCACCGAACACACCCGCAATCTCGAACGGCTGGTGCGCGAAAAATCCGCCCGCCTGGTCGAGATGGAGCGCCGCATGGCCGTGGGGCAGGCCGTGGAGGGCGTGGCCAGCGCCATCGAGGGGCTCATTGCCTCCTTCGACCAGGGACCCAGCTATTTCAACCAGATGCCCTGCTGCATCGTCATCCACAACCGCTACCTCGAAATCGTGGCCGTAAACACCCTGGGCCGGCAGCGCCTGGGCGAGGTGGTGGGCAAGATGAGCTGGGAACTCTACGCCGACCGTCAGGGCAGCGGCAACGCCTGCCCGGTCTGGCGCACCGTGGAACAAGGCCAGGGCCAGCGCGGCCGCGAGACCTTCCGCGACAAGGACGGCCGCGAGATTCCGGTGCTGATCCATACCGCCCCGGTCTTCGGCACGGACGGCCAGGTGGAGCTGGTCATCGAGATCGCCGCCGACGTGGCCGAGGTGGGCCGGCTCCAGGAAGAGCTGCGGGCCGTGCGCGAGAAATTCCAGCGCCTGTTCGACGCCGTGCCCTGCGCCATCGCCGTGCTGGACCAGGACTTCACCGTGGTCGAAGCCAACCGCCAATGGCGCGCCGACTTCGGCGAGGCCGAAACCGGCCCCTGCCACAAACTGTTTGCCCACCGCGACGACCCCTGCGAACACTGCCCGGCCGAAAGCTCCTTCCACGACGGCGCGCCCCACGAAGGCGAAACTGTCGTGTCCACCCGCTGCGGCGCGGCCAAAAACATGTGGCTTCGCACCGCCCCCATCCCCGACGCCACAGGCGAAACCAGCCAGGTCATCGAAATCGCCGCCGACATCACCCCCATCCGGGCCCTGCAAGACCACCTCGCATCGCTTGGGCTCATGCTCGGCTCCATGTCCCACGGCGTCAAAGGCCTGCTCACCTCCCTCGACGGCGGCATGTTCAAGGTCGAAACCGGACTGTCCCGCGAGGACTGGACCCGCGTGCGCGACGGTTGGGGCGTGGTGTCCGACAAGATCGGACGCATCCGCAACATGGTGCTCGACATCCTGTGGTACGCCAAATCGCGCGAACCCGAGCTCTCCCCCGTCTCCATCGAAACCTTCGCCCGCGATCTGGCCGGCATCGTCGAACCCAAGGCCCAAAGCCGCGACGTGGCCTTCATCCTGCGCCTGGGCGAGGCCGCAGGCACGCTGCCCATGGACGAGACGGCGCTCACCTCGGCCATGGTCAACCTGCTCGAAAACGCCGTGGATGCCTGCGCCGAGGACAAGGCCAAGGCCTTCCACGAAGTGACCCTGACCGTGGAAGCCACGGCCGAGGCCGTGACCTTCGTGGTCGCCGACAACGGCGTCGGCATGGACCAGTCCACCCGGGAACGCATGTTTACGCTCTTTTTCTCCTCCAAAGGCTCGCGCGGCACCGGACTGGGGCTTTTCATCGCCAACCAGATCGTGGCCCAGCACGGAGGCTCCATCGCCGTGACCTCCGAACCCGGCGTCGGCAGCGCCATCGCCGTGCGCCTGCCGCGCGGCGCTAGCGTTTGCAGTTAG