Ejemplo n.º 1
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def from_transcript(transcript, params):
    """It does workflow for creating sh-miR from transcript

    Args:
        transcript: name of NCBI transcript
        params: dict with optional arguments:
            * min_gc -- Minimal "GC" content in strand
                default: 40
            * max_gc -- Maximal "GC" content in strand
                default: 60
            * max_offtarget -- Maximal offtarget in strand
                default: 10
            * mirna_name -- The name of miRNA backbone to use
                default: 'all'
            * stymulators -- one of "yes", "no", "no_difference"
                default: 'no_difference'

    Returns:
        None
    """
    return wait_until_task(
        creator("from_transcript_create", transcript,
                params=params), lambda task_id, **kwargs: checker(
                    "from_transcript_check", task_id, **kwargs),
        from_transcript_result)
Ejemplo n.º 2
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def from_transcript(transcript, params):
    """It does workflow for creating sh-miR from transcript

    Args:
        transcript: name of NCBI transcript
        params: dict with optional arguments:
            * min_gc -- Minimal "GC" content in strand
                default: 40
            * max_gc -- Maximal "GC" content in strand
                default: 60
            * max_offtarget -- Maximal offtarget in strand
                default: 10
            * mirna_name -- The name of miRNA backbone to use
                default: 'all'
            * immuno -- one of "yes", "no", "no_difference"
                default: 'no_difference'

    Returns:
        None
    """
    return wait_until_task(
        creator("from_transcript_create", transcript, params=params),
        lambda task_id, **kwargs: checker("from_transcript_check", task_id, **kwargs),
        from_transcript_result,
    )
Ejemplo n.º 3
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def mfold(sequence):
    """It does all workflow for mfold task
        * creates task
        * wait until it's done
        * gets result(s)

    Args:
        sequence: Sequence which we would like to fold via mfold

    Returns:
        None
    """
    return wait_until_task(
        creator("mfold_create", sequence),
        lambda task_id, **kwargs: checker("mfold_check", task_id, **kwargs),
        mfold_result)
Ejemplo n.º 4
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def from_sirna(sequences):
    """It does workflow for creating sh-miR from siRNA sequence(s)
        * creates task
        * wait until it's done
        * gets result(s)

    Args:
        sequences: one siRNA strand (active) or two siRNA strands separated by space.
            First strand is active, both are in 5-3 orientation.

    Returns:
        None
    """
    return wait_until_task(
        creator("from_sirna_create",
                sequences), lambda task_id, **kwargs: checker(
                    "from_sirna_check", task_id, **kwargs), from_sirna_result)
Ejemplo n.º 5
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def mfold(sequence):
    """It does all workflow for mfold task
        * creates task
        * wait until it's done
        * gets result(s)

    Args:
        sequence: Sequence which we would like to fold via mfold

    Returns:
        None
    """
    return wait_until_task(
        creator("mfold_create", sequence),
        lambda task_id, **kwargs: checker("mfold_check", task_id, **kwargs),
        mfold_result,
    )
Ejemplo n.º 6
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def from_sirna(sequences):
    """It does workflow for creating sh-miR from siRNA sequence(s)
        * creates task
        * wait until it's done
        * gets result(s)

    Args:
        sequences: one siRNA strand (active) or two siRNA strands separated by space.
            First strand is active, both are in 5-3 orientation.

    Returns:
        None
    """
    return wait_until_task(
        creator("from_sirna_create", sequences),
        lambda task_id, **kwargs: checker("from_sirna_check", task_id, **kwargs),
        from_sirna_result,
    )