Source code for tmtk.params.AnnotationParams

from .ParamsBase import ParamsBase
import os

[docs]class AnnotationParams(ParamsBase): @property def mandatory(self): return {'PLATFORM': { 'helptext': 'Short identifier for platform.' }, 'TITLE': { 'helptext': 'Platform description.' }, 'ANNOTATIONS_FILE': { 'variable_type': 'filename', 'helptext': 'Points to the annotations file.' } } @property def optional(self): return {'ORGANISM': { 'helptext': 'Usually Homo sapiens.' }, 'GENOME_RELEASE': { 'helptext': 'Something like hg19 or hg38. Only required when' ' genomic coordinates are provided in the file.' }, }
[docs] def is_viable(self): """ :return: True if both the platform is set and the annotations file is located, else returns False. """ if self.get('ANNOTATIONS_FILE') and self.get('PLATFORM'): file_found = os.path.exists(os.path.join(self.dirname, self.ANNOTATIONS_FILE)) return file_found else: return False