bioprov 0.1.13

BioProv - Provenance capture for bioinformatics workflows

BioProv - W3C-PROV provenance documents for bioinformatics

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BioProv is a Python library for W3C-PROV representation of biological data. It enables you to quickly write workflows and to describe relationships between samples, files, users and processes.

Please see the tutorials for a more detailed introduction.

>>> import bioprov as bp

# Create samples and file objects
>>> sample = bp.Sample("mysample")
>>> genome = bp.SequenceFile("mysample.fasta", "genome")
>>> sample.add_files(genome)

# Create programs
>>> output = sample.files["blast_out"] = bp.File("mysample.blast.tsv", "blast_out")
>>> blast = bp.Program("blastn", params={"-query": sample.files["genome"], "-db": "mydb.fasta", "-out": output})

# Run programs
>>> blast.run(sample=sample)  # Or sample.run(program=blast)

BioProv also has a command-line application to run preset workflows.

$ bioprov -h
usage: bioprov [-h] {genome_annotation,kaiju} ...

BioProv command-line application. Choose a workflow to begin.

optional arguments:
  -h, --help            show this help message and exit

workflows:
  {genome_annotation,kaiju}

BioProv is built with the Biopython and Pandas libraries.

You can import data into BioProv using Pandas objects.

# Read csv straight into BioProv
>>> samples = bp.read_csv("my_dataframe.tsv", sep="\t", sequencefile_cols="assembly")

# Alternatively, use a pandas DataFrame
>>> df = pd.read_csv("my_dataframe.tsv", sep="\t")

# [...] manipulate your df
>>> df["assembly"] = "assembly_directory/" + df["assembly"]

# Now load from your df
>>> samples = bp.from_df(df, sequencefile_cols="assembly", source_file="my_dataframe.tsv")

# `samples` becomes a Project dict-like object
>>> sample1 = samples['sample1']

BioProv 'SequenceFile' objects contains records formatted as Biopython SeqRecords:

>>> type(sample1)
Bio.SeqRecord.SeqRecord

BioProv objects can be imported or exported as JSON objects.

>>> sample1.to_json(), samples.to_json()

Installation

# Install from pip
$ pip install bioprov

# Or install from source
$ git clone https://github.com/vinisalazar/bioprov  # download
$ cd bioprov; pip install .                         # install
$ pytest                                            # test

Important! BioProv requires Prodigal to be tested. Otherwise tests will fail.

Contributions are welcome!

BioProv is in active development and no warranties are provided (please see the License).