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: 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: InvestigationInfo, output_file: TextIO, quote=None, lineterminator=None)[source]
Construct from file-like object
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)