Skip to content

identifiers_form() function does not work well. #35

Open
@136s

Description

@136s

When I input expression data to analysis.identifiers_form() function, "Status code returned a value of 415" raises.

The following code shows the difference from using the analysis.identifiers_url() function using the expample of Microarray data.

Reproducible code:

from subprocess import run
from reactome2py import analysis

expression_url = "https://gist.githubusercontent.com/136s/144efdf249c135717a52f2a2c257cd8e/raw/e7633a3c7a17802bf37ab895c65f511610f14d74/Probeset.tsv"

run("curl -O {}".format(expression_url), shell=True)
form_res = analysis.identifiers_form("Probeset.tsv")
print(f"{form_res=}")

url_res = analysis.identifiers_url(expression_url)
print(f"{url_res=}")

results:

Status code returned a value of 415
form_res=None
url_res={'summary': {'token': 'MjAyNDAxMjIwMTM0MjNfOTQ5OQ%3D%3D', 'projection': False, 'interactors': False, 'type': 'EXPRESSION', 'sampleName': 'Probeset', 'text': True, 'includeDisease': True}, 'expression': {'columnNames': ['10h_control', '10h', '14h', '18h', '24h'], 'min': 2.812419, 'max': 13.505858}, 'identifiersNotFound': 34, 'pathwaysFound': 1408, 'pathways': [{'stId': 'R-HSA-5651801', 'dbId': 5651801, 'name': 'PCNA-Dependent Long Patch Base Excision Repair', 'species': {'dbId': 48887, 'taxId': '9606', 'name': 'Homo sapiens'}, 'llp': True, 'entities': {'resource': 'TOTAL', 'total': 23, 'found': 19, 'ratio': 0.001487325400931195, 'pValue': 1.1102230246251565e-16, 'fdr': 7.771561172376096e-16, 'exp': [8.307529157894736, 7.673377315789473, 7.888002789473684, 7.8596394736842115, 7.299411473684212]}, 'reactions': {'resource': 'TOTAL', 'total': 6, 'found': 6, 'ratio': 0.00040752564015485973}, 'inDisease': False}], 'resourceSummary': [{'resource': 'TOTAL', 'pathways': 1408, 'filtered': 1408}, {'resource': 'UNIPROT', 'pathways': 1408, 'filtered': 1408}], 'speciesSummary': [{'dbId': 48887, 'taxId': '9606', 'name': 'Homo sapiens', 'pathways': 1408, 'filtered': 1408}], 'warnings': []}

version:

  • python: 3.11.0
  • reactome2py: 3.0.0

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions