flowbio
=======
A client for the Flow API.
.. code-block:: python
import flowbio
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={
"category": "RNA-Seq",
"strandedness": "unstranded",
}
)
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},
)
Raw data
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"description": "flowbio\n=======\n\nA client for the Flow API.\n\n.. code-block:: python\n \n import flowbio\n\n client = flowbio.Client()\n client.login(\"your_username\", \"your_password\")\n\n # Upload standard data\n data = client.upload_data(\"/path/to/file.fa\", progress=True, retries=5)\n print(data)\n\n # Upload sample\n sample = client.upload_sample(\n \"My Sample Name\",\n \"/path/to/reads1.fastq.gz\",\n \"/path/to/reads2.fastq.gz\", # optional\n progress=True,\n retries=5,\n metadata={\n \"category\": \"RNA-Seq\",\n \"strandedness\": \"unstranded\",\n }\n )\n print(sample)\n\n # Upload multiplexed\n multiplexed = client.upload_multiplexed(\n \"/path/to/reads.fastq.gz\",\n progress=True,\n retries=5,\n )\n print(multiplexed)\n\n # Upload annotation\n annotation = client.upload_annotation(\n \"/path/to/annotation.csv\",\n progress=True,\n retries=5,\n )\n print(annotation)\n\n # Run pipeline\n execution = client.run_pipeline(\n \"RNA-Seq\",\n \"3.8.1\",\n \"23.04.3\",\n params={\"param1\": \"param2\"},\n data_params={\"fasta\": 123456789},\n )\n\n\n",
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JSON
