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Merge pull request #120 from jiaan-yu/rnaseq
Add RNASeq Fusion Workflow related tools
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‎janis_bioinformatics/tools/__init__.py‎

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BioinformaticsWorkflow,
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)
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from janis_bioinformatics.tools import (
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arriba,
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babrahambioinformatics,
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biobambam,
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bcftools,

‎janis_bioinformatics/tools/arriba/__init__.py‎

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from .run_arriba.versions import RunArriba_2_1_0, RunArriba_1_1_0
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from .draw_fusions.versions import ArribaDrawFusions_2_1_0, ArribaDrawFusions_1_1_0

‎janis_bioinformatics/tools/arriba/base.py‎

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from abc import ABC, abstractmethod
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from janis_bioinformatics.tools import BioinformaticsTool
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class ArribaBase(BioinformaticsTool, ABC):
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def tool_provider(self):
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return "Arriba"
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@classmethod
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def base_command(cls):
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return ["", cls.arriba_command()]
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@classmethod
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@abstractmethod
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def arriba_command(cls):
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raise Exception("Unknown error occured")
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def inputs(self):
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return []
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def doc(self):
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return """\
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Arriba is a command-line tool for the detection of gene fusions from RNA-Seq \
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data. It was developed for the use in a clinical research setting.""".strip()
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@abstractmethod
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def container(self):
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raise Exception(
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"An error likely occurred when resolving the method order for docker for the facets classes "
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"or you're trying to execute the docker method of the base class (ie, don't do that). "
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"The method order resolution must preference facets subclasses, "
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"and the subclass must contain a definition for docker."
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)

‎janis_bioinformatics/tools/arriba/draw_fusions/__init__.py‎

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‎janis_bioinformatics/tools/arriba/draw_fusions/base.py‎

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from abc import ABC
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from datetime import datetime
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from janis_bioinformatics.tools.bioinformaticstoolbase import BioinformaticsTool
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from janis_unix import Csv, Tsv
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from janis_bioinformatics.data_types import BamBai
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from janis_core import (
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CommandTool,
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ToolInput,
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ToolOutput,
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File,
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Boolean,
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String,
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Int,
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Double,
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Float,
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InputSelector,
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Filename,
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ToolMetadata,
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InputDocumentation,
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Array,
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)
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from janis_bioinformatics.tools.arriba.base import ArribaBase
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class ArribaDrawFusionsBase(ArribaBase, ABC):
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@classmethod
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def arriba_command(self):
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return "/usr/local/bin/draw_fusions.R"
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def friendly_name(self) -> str:
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return "Arriba: DrawFusions"
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def tool(self) -> str:
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return "ArribaDrawFusions"
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def inputs(self):
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return [
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ToolInput(
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tag="annotation",
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input_type=File(),
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prefix="--annotation=",
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separate_value_from_prefix=False,
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doc="exonsFile",
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),
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ToolInput(
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tag="fusions",
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input_type=File(),
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prefix="--fusions=",
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separate_value_from_prefix=False,
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doc="fusionsFile",
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),
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ToolInput(
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tag="outputFilename",
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input_type=Filename(extension=".pdf"),
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prefix="--output=",
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separate_value_from_prefix=False,
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doc="outputFile",
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),
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ToolInput(
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tag="alignments",
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input_type=BamBai(optional=True),
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prefix="--alignments=",
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separate_value_from_prefix=False,
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doc="alignmentsFile",
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),
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ToolInput(
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tag="cytobands",
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input_type=File(optional=True),
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prefix="--cytobands=",
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separate_value_from_prefix=False,
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doc="cytobandsFile",
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),
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ToolInput(
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tag="minConfidenceForCircosPlot",
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input_type=String(optional=True),
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prefix="--minConfidenceForCircosPlot=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="proteinDomains",
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input_type=File(optional=True),
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prefix="--proteinDomains=",
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separate_value_from_prefix=False,
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doc="proteinDomainsFile",
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),
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ToolInput(
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tag="squishIntrons",
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input_type=Boolean(optional=True),
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prefix="--squishIntrons=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="printExonLabels",
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input_type=Boolean(optional=True),
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prefix="--printExonLabels=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="renderThreeDEffect",
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input_type=Boolean(optional=True),
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prefix="--render3dEffect=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="pdfWidth",
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input_type=Float(optional=True),
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prefix="--pdfWidth=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="pdfHeight",
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input_type=Float(optional=True),
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prefix="--pdfHeight=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="color_one",
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input_type=String(optional=True),
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prefix="--color1=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="color_two",
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input_type=String(optional=True),
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prefix="--color2=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="mergeDomainsOverlappingBy",
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input_type=Float(optional=True),
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prefix="--mergeDomainsOverlappingBy=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="optimizeDomainColors",
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input_type=Boolean(optional=True),
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prefix="--optimizeDomainColors=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="fontSize",
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input_type=Int(optional=True),
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prefix="--fontSize=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="showIntergenicVicinity",
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input_type=Int(optional=True),
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prefix="--showIntergenicVicinity=",
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separate_value_from_prefix=False,
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doc="",
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),
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ToolInput(
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tag="transcriptSelection",
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input_type=String(optional=True),
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prefix="--transcriptSelection=",
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separate_value_from_prefix=False,
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doc="",
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),
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]
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def outputs(self):
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return [ToolOutput("out", File, selector=InputSelector("outputFilename"))]
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def bind_metadata(self):
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return ToolMetadata(
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contributors=["Jiaan Yu"],
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dateCreated=datetime(2021, 3, 15),
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dateUpdated=datetime(2021, 3, 15),
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documentation="""
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Arriba comes with an R script draw_fusions.R that renders publication-quality
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visualizations of the transcripts involved in predicted fusions. It generates
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a PDF file with one page for each predicted fusion. Each page depicts the
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fusion partners, their orientation, the retained exons in the fusion
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transcript, statistics about the number of supporting reads, and - if the
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column fusion_transcript has a value - an excerpt of the sequence around the
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breakpoint.
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""",
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)

‎janis_bioinformatics/tools/arriba/draw_fusions/versions.py‎

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from .base import ArribaDrawFusionsBase
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from ..versions import Arriba_1_1_0, Arriba_2_1_0
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class ArribaDrawFusions_1_1_0(Arriba_1_1_0, ArribaDrawFusionsBase):
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pass
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class ArribaDrawFusions_2_1_0(Arriba_2_1_0, ArribaDrawFusionsBase):
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pass

‎janis_bioinformatics/tools/arriba/run_arriba/__init__.py‎

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