Writers

Classes to write AltamISA model files to ISA-Tab investigation, study and assay files. Note that writers can issue warnings, see Writers on how to capture them properly.

altamisa.isatab.InvestigationWriter

class altamisa.isatab.InvestigationWriter(investigation: altamisa.isatab.models.InvestigationInfo, output_file: TextIO, quote=None, lineterminator=None)[source]

Main class to write an investigation file from an InvestigationInfo object.

Parameters:
  • investigation (models.InvestigationInfo) – The investigation model to write
  • output_file (TextIO) – Output ISA-Tab investigation file
  • quote (str) – Optional quoting character (none by default)
  • lineterminator (str) – Optional line terminator (OS specific by default)
classmethod from_stream(investigation: altamisa.isatab.models.InvestigationInfo, output_file: TextIO, quote=None, lineterminator=None)[source]

Construct from file-like object

write()[source]

Write investigation file

altamisa.isatab.AssayWriter

class altamisa.isatab.AssayWriter(study_or_assay: NamedTuple, output_file: TextIO, quote=None, lineterminator=None)[source]

Class that writes a file from an Assay object.

Parameters:
  • study_or_assay (models.Assay) – The assay model to write
  • output_file (TextIO) – Output ISA-Tab assay file
  • quote (str) – Optional quoting character (none by default)
  • lineterminator (str) – Optional line terminator (OS specific by default)

altamisa.isatab.StudyWriter

class altamisa.isatab.StudyWriter(study_or_assay: NamedTuple, output_file: TextIO, quote=None, lineterminator=None)[source]

Class that writes a file from an Study object.

Parameters:
  • study_or_assay (models.Study) – The study model to write
  • output_file (TextIO) – Output ISA-Tab study file
  • quote (str) – Optional quoting character (none by default)
  • lineterminator (str) – Optional line terminator (OS specific by default)