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miEAA command line interface and api wrapper

Project description

miEAA CLI and API Wrapper

The miRNA Enrichment Analysis and Annotation Tool (miEAA) facilitates the functional analysis of sets of miRNAs.
This package provides a command line interface and wrapper for the miEAA API.

To learn more about miEAA or to utilize our online interface, please visit our web server.
All miEAA tools are provided and hosted by the Chair for Clinical Bioinformatics at Saarland University.

This package allows users to execute miEAA directly from the command line:

$ mieaa -h

An API wrapper is also provided for scripting purposes:

from mieaa import API

mieaa_api = API()

Installation

Dependencies:

  • Python >= 3.5
  • Requests >= 2.19

pip

$ pip install mieaa

Conda Anaconda-Server Badge

$ conda install -c ccb-sb mieaa

Examples

For example usage, see the example Python script.
Using the reticulate library, users can utilize our package in R (Python installation is still required). As such, an example R script is also provided.

Command Line Interface

Commands can be invoked using mieaa SUBCOMMAND.
Help and options for all subcommands can be invoked using mieaa SUBCOMMAND -h

Subcommand Description
to_precursor Convert miRNAs to precursors
to_mirna Convert precursors to miRNAs
convert_mirbase Convert mirBase version
gsea Run Gene Set Enrichment Analysis
ora Run Over-representation Analysis

Commands may require specifying if input is from a list of strings or a file (see -m/M in examples, below).
In such cases, the flag letter is identical, with lowercase specifying string/list, and uppercase specifying a file.

Important Notes

Specifying precursors
For subcommands where you need to specify precursor or mature, mature is always assumed unless the --precursor (-p) flag is set.

Mutually exclusive options
Each subcommand requires either --mirna-set (-m) or --mirna-set-file (-M) to be specified. Enrichment analyses also require similarly behaving arguments for categories, and optionally for reference sets in the case of ORA.

  • miea SUBCOMMAND --mirna-set MIRNA [MIRNA ...]
  • miea SUBCOMMAND --mirna-set MIRNAS_STRING
  • miea SUBCOMMAND --mirna-set-file MIRNA_FILE

Converting miRNA -> precursor

  • mieaa to_precursor [-m | -M] -FLAGS
$ mieaa to_precursor -m hsa-miR-20b-5p hsa-miR-144-5p --tabsep --unique
$ mieaa to_precursor -m 'hsa-miR-20b-5p,hsa-miR-144-5p' -o precursors.txt
$ mieaa to_precursor -M mirnas.txt --outfile precursors.txt

Converting between precursor -> miRNA

  • mieaa to_mirna [-m | -M] -FLAGS
$ mieaa to_mirna -m hsa-mir-20b hsa-mir-144 --tabsep --unique
$ mieaa to_mirna -m 'hsa-mir-20b,hsa-mir-144' -o mirnas.txt
$ mieaa to_mirna -M precursors.txt --outfile mirnas.txt

Converting miRBase version

mieaa convert_mirbase FROM_VERSION [-m | -M] -FLAGS

$ mieaa convert_mirbase 16 -m hsa-miR-642b,hsa-miR-550b
$ mieaa convert_mirbase 16 --to 22 -m hsa-miR-642b hsa-miR-550b
$ mieaa convert_mirbase 16  -M version_16.txt -o version_22.txt

Gene Set Enrichment Analysis (GSEA)

mieaa gsea SPECIES [-m | -M] [-c | -C] -FLAGS

Species can be specified as hsa, mmu, or rno. The category flags (-c -C) behave identically to the miRNA set flags (-m -M).

$ mieaa gsea hsa --precursors -M precursors.txt -C categories.txt -o results.csv
$ mieaa gsea hsa -p -M precursors.txt -c HMDD MNDR > results.csv
$ mieaa gsea mmu -M mirnas.txt -C categories.txt --adjustment none
$ mieaa gsea rno -M mirnas.txt -C categories.txt -a bonferonni --json -o results.json

Over-representation Analysis (ORA)

mieaa ora SPECIES [-m | -M] [-c | -C] -FLAGS

Species can be specified as hsa, mmu, or rno. The category flags (-c -C) and reference set flags (-r -R) behave identically to the miRNA set flags (-m -M).

$ mieaa ora hsa --precursors -M precursors.txt -C categories.txt > results.csv
$ mieaa ora hsa -p -M precursors.txt -c HMDD MNDR -o results.csv
$ mieaa ora hsa -p -M precursors.txt -C categories.txt -R reference.txt
$ mieaa ora mmu -M mirnas.txt -C categories.txt --adjustment none
$ mieaa ora rno -M mirnas.txt -C categories.txt -a bonferonni --json -o results.json

API Wrapper

The miEAA API can be easily utilized via the API class.

API Class

from mieaa import API

mieaa_api = API()

Attributes

job_id - unique job identifier tied to this instance after starting an enrichment analysis

Methods

convert_mirbase_version

mieaa_api.convert_mirbase_version(mirnas, from_version, to_version, input_type, to_file='', output_format='oneline')

parameters

  • mirnas - str, list-like, or file-object
    • set of either mature miRNAs or precursors we want to convert
  • from_version - float
    • miRBase version we want to convert given set from
  • to_version - float
    • miRBase version we want to convert given set to
  • input_type - 'precursor' or 'mirna'
    • Whether the provided set includes precursors or mature miRNAs
  • to_file - file-object or str
    • If provided, converted miRNA/precursor set will be saved
  • output_format - 'oneline' or 'tabsep'
    • 'oneline': Text containing only converted miRNAs/precursors
    • 'tabsep': Tab-separated input and output miRNAs/precursors

return

list - converted miRNAs/precursors

convert_mirna_to_precursor

mieaa_api.convert_mirna_to_precursor(mirnas,  to_file='', output_format='oneline', conversion_type='all')

parameters

  • mirnas - str, list-like, or file-object
    • set of either mature miRNAs or precursors we want to convert
  • to_file - file-object or str
    • If provided, converted miRNA/precursor set will be saved
  • output_format - 'oneline' or 'tabsep'
    • 'oneline': Text containing only converted miRNAs/precursors
    • 'tabsep': Tab-separated input and output miRNAs/precursors
  • conversion_type: 'all' or 'unique'
    • 'all': Output all newly converted precursors
    • 'unique': Only output precursors with unique mappings

return

list - newly converted precursors

convert_precursor_to_mirna

mieaa_api.convert_precursor_to_mirna(mirnas,  to_file='', output_format='oneline', conversion_type='all')

parameters

  • mirnas - str, list-like, or file-object
    • set of either mature miRNAs or precursors we want to convert
  • to_file - file-object or str
    • If provided, converted miRNA/precursor set will be saved
  • output_format - 'oneline' or 'tabsep'
    • 'oneline': Text containing only converted miRNAs/precursors
    • 'tabsep': Tab-separated input and output miRNAs/precursors
  • conversion_type: 'all' or 'unique'
    • 'all': Output all newly converted miRNAs
    • 'unique': Only output miRNAs with unique mappings

return

list - newly converted miRNAs

run_gsea

mieaa_api.run_gsea(test_set, categories, input_type, species, p_value_adjustment='fdr', significance_level=0.05, independent_p_adjust=True, threshold_level=2)

parameters

  • test_set - str, list-like, or file-object
    • set of either mature miRNAs or precursors we want to convert
  • categories - str, list-like, or file-object
    • set of categories use in enrichment analysis
  • input_type - 'precursor' or 'mirna'
    • Whether the provided set includes precursors or mature miRNAs
  • species - 'hsa', 'mmu', 'rno'
    • 'hsa': Homo sapiens
    • 'mmu': Mus musculus
    • 'rno': Rattus norvegicus
  • p_value_adjustment - 'none','fdr','bonferroni','BY','holm','hochberg','hommel'
    • 'none' - No adjustment
    • 'fdr' - FDR (Benjamini-Hochberg) adjustment
    • 'bonferroni' - Bonferroni adjustmen
    • 'BY' - Benjamini-Yekutieli adjustment
    • 'hochberg' - Hochberg adjust
    • 'holm' - Holm adjustment
    • 'hommel' - Hommel adjustment
  • significance_level - float
    • Filter out p-values above specified level
  • independent_p_adjust - bool
    • True: Adjust p-values for each category independently
    • False: Adjust p-values for all categories collectively
  • threshold_level - int
    • Filter out subcategories containing less than this many miRNAs/precursors

return

requests.Response - API response

run_ora

mieaa_api.run_ora(test_set, categories, input_type, species, reference_set='', p_value_adjustment='fdr', significance_level=0.05, independent_p_adjust=True, threshold_level=2)

parameters

  • test_set - str, list-like, or file-object
    • set of either mature miRNAs or precursors we want to convert
  • categories - str, list-like, or file-object
    • set of categories use in enrichment analysis
  • input_type - 'precursor' or 'mirna'
    • Whether the provided set includes precursors or mature miRNAs
  • species - 'hsa', 'mmu', 'rno'
    • 'hsa': Homo sapiens
    • 'mmu': Mus musculus
    • 'rno': Rattus norvegicus
  • reference_set - str, list-like, or file-object
    • If specified, use as background reference set
  • p_value_adjustment - 'none','fdr','bonferroni','BY','holm','hochberg','hommel'
    • 'none' - No adjustment
    • 'fdr' - FDR (Benjamini-Hochberg) adjustment
    • 'bonferroni' - Bonferroni adjustmen
    • 'BY' - Benjamini-Yekutieli adjustment
    • 'hochberg' - Hochberg adjust
    • 'holm' - Holm adjustment
    • 'hommel' - Hommel adjustment
  • significance_level - float
    • Filter out p-values above specified level
  • independent_p_adjust - bool
    • True: Adjust p-values for each category independently
    • False: Adjust p-values for all categories collectively
  • threshold_level - int
    • Filter out subcategories containing less than this many miRNAs/precursors

return

requests.Response - API response

get_enrichment_Parameters

mieaa_api.get_enrichment_Parameters()

return

dict - Parameters that were provided when calling run_gsea() or run_ora()

get_results

mieaa_api.get_results(results_format='json', check_progress_interval=5)

parameters

  • results_format - 'json' or 'csv'
    • Whether to retrieve results as json or as a csv string
  • check_progress_interval - float
    • How many seconds to wait in between checking if results have finished computing

return

list or str containing the results

save_enrichment_results

mieaa_api.save_enrichment_results(save_file, file_type='csv', check_progress_interval=5)

parameters

  • save_file - str or file-object
    • Where to save the results
  • file_type - 'csv' or 'json'
    • File format we want to save results as
  • check_progress_interval - float
    • How many seconds to wait in between checking if results have finished computing

return

  • str - results as they were written to file

invalidate

Invalidate this instance. Previous results become irretrievable, but can now be used to run a fresh analysis.

mieaa_api.invalidate()

return

None

get_enrichment_categories

mieaa_api.get_enrichment_categories(input_type, species, with_suffix=False)

parameters

  • input_type - 'precursor' or 'mirna'
    • Whether the provided set includes precursors or mature miRNAs
  • species - 'hsa', 'mmu', 'rno'
    • 'hsa': Homo sapiens
    • 'mmu': Mus musculus
    • 'rno': Rattus norvegicus
  • with_suffix - bool
    • Whether to include '_precursor' or '_mature' suffix in category names

return dict - keys are the category names, values are a short description

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