shmir_client module

shmir_client.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

shmir_client.from_sirna_result(task_id)

Gets sh-miR result created from siRNA via task_id

Args:

task_id: Id of task which was given by RESTful API

Returns:

None

shmir_client.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

shmir_client.from_transcript_result(task_id)

Gets sh-miR result created from transcript via task_id

• creates task
• wait until it’s done
• gets result(s)

Args:

task_id: Id of task which was given by RESTful API

Returns:

None

shmir_client.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

shmir_client.mfold_result(task_id, zipname='now.zip', path='./results/mfold/', verbose=True)

Gets mfold result via task_id

Args:

task_id: Id of task which was given by RESTful API zipname: Name of zip file in which client will save results.

After save this file is removed

path: Path where results should be stored verbose: Bool which tells if function should print what she actualy does

Returns:

None