Parsers¶
Classes to read data from ISA-Tab investigation, study and assay files and create the corresponding AltamISA models. Note that parsers can issue warnings, see Validators on how to capture them properly.
Contents
altamisa.isatab.InvestigationReader¶
altamisa.isatab.AssayReader¶
-
class
altamisa.isatab.
AssayReader
(study_id: str, assay_id: str, input_file: TextIO, filename=None)[source]¶ Read an ISA-TAB assay file (
a_*.txt
) into aAssay
object.This is the main facade class for reading assay objects. Prefer it over using the more low-level code.
Parameters: - study_id (str) – Unique identifier for the study, needed to disambiguate nodes between files.
- assay_id (str) – Unique identifier for the assay, needed to disambiguate nodes between files.
- input_file (TextIO) – ISA-Tab assay file
altamisa.isatab.AssayRowReader¶
-
class
altamisa.isatab.
AssayRowReader
(study_id: str, assay_id: str, input_file: TextIO, filename: str)[source]¶ Read an ISA-TAB assay file (
a_*.txt
) into a tabular/object representation.This is a more low-level part of the interface. Please prefer using :py:AssayReader: over using this class.
Parameters: - study_id (str) – Unique identifier for the study, needed to disambiguate nodes between files.
- assay_id (str) – Unique identifier for the assay, needed to disambiguate nodes between files.
- input_file (TextIO) – ISA-Tab assay file
altamisa.isatab.StudyReader¶
-
class
altamisa.isatab.
StudyReader
(study_id: str, input_file: TextIO, filename=None)[source]¶ Read an ISA-TAB study file (
s_*.txt
) into aStudy
object.This is the main facade class for reading study objects. Prefer it over using the more low-level code.
Parameters: - study_id (str) – Unique identifier for the study, needed to disambiguate nodes between files.
- input_file (TextIO) – ISA-Tab study file
altamisa.isatab.StudyRowReader¶
-
class
altamisa.isatab.
StudyRowReader
(study_id: str, input_file: TextIO, filename: str)[source]¶ Read an ISA-TAB study file (
s_*.txt
) into a tabular/object representation.This is a more low-level part of the interface. Please prefer using :py:StudyReader: over using this class.
Parameters: - study_id (str) – Unique identifier for the study, needed to disambiguate nodes between files.
- input_file (TextIO) – ISA-Tab study file