flowbio
A client for the Flow API. Full documentation is available at https://goodwright.github.io/flowbio/.
import flowbio
# NB: this client is being deprecated. Please use the v2 client instead. See the [v2 documentation](https://goodwright.github.io/flowbio/v2/) for details.
client = flowbio.Client()
client.login("your_username", "your_password")
# Upload standard data
data = client.upload_data("/path/to/file.fa", progress=True, retries=5)
print(data)
# Upload sample
sample = client.upload_sample(
"My Sample Name",
"/path/to/reads1.fastq.gz",
"/path/to/reads2.fastq.gz", # optional
progress=True,
retries=5,
metadata={
"sample_type": "RNA-Seq",
"scientist": "Charles Darwin",
"type_specific_metadata": '{"strandedness": "reverse"}',
}
)
print(sample)
# Upload multiplexed
multiplexed = client.upload_multiplexed(
"/path/to/reads.fastq.gz",
progress=True,
retries=5,
)
print(multiplexed)
# Upload annotation
annotation = client.upload_annotation(
"/path/to/annotation.csv",
progress=True,
retries=5,
)
print(annotation)
# Run pipeline
execution = client.run_pipeline(
"RNA-Seq",
"3.8.1",
"23.04.3",
params={"param1": "param2"},
data_params={"fasta": 123456789},
)
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