Headers¶
This module contains code for the representation of headers from study and assay files and parsing thereof.
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class
altamisa.isatab.headers.
ColumnHeader
(column_type, col_no, span)[source]¶ Column header in a study or assay file
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column_type
= None¶ The type of this header
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col_no
= None¶ The column number this header refers to
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span
= None¶ Number of columns this header spans
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term_source_ref_header
= None¶ Link to the TermSourceRefHeader to use
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unit_header
= None¶ Link to the UnitHeader to use
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class
altamisa.isatab.headers.
SimpleColumnHeader
(col_no)[source]¶ Base class for simple column headers.
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column_type
= None¶ The value to use for the
type
argument.
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class
altamisa.isatab.headers.
ExtractHeader
(col_no)[source]¶ Extract header in an assay
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column_type
= 'Extract Name'¶
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class
altamisa.isatab.headers.
LabeledExtractHeader
(col_no)[source]¶ Labeled Extract header in an assay
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column_type
= 'Labeled Extract Name'¶
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class
altamisa.isatab.headers.
LibraryHeader
(col_no)[source]¶ Library header in an assay
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column_type
= 'Library Name'¶
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class
altamisa.isatab.headers.
SampleHeader
(col_no)[source]¶ Sample header in a study or assay
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column_type
= 'Sample Name'¶
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class
altamisa.isatab.headers.
SourceHeader
(col_no)[source]¶ Source header in a study
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column_type
= 'Source Name'¶
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class
altamisa.isatab.headers.
ArrayDataFileHeader
(col_no)[source]¶ ArrayData header in an assay
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column_type
= 'Array Data File'¶
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class
altamisa.isatab.headers.
ArrayDataMatrixFileHeader
(col_no)[source]¶ ArrayData Matrix File header in an assay
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column_type
= 'Array Data Matrix File'¶
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class
altamisa.isatab.headers.
ArrayDesignFileHeader
(col_no)[source]¶ ArrayDesignFile header in an assay
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column_type
= 'Array Design File'¶
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class
altamisa.isatab.headers.
DerivedArrayDataFileHeader
(col_no)[source]¶ DerivedArrayData header in an assay
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column_type
= 'Derived Array Data File'¶
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class
altamisa.isatab.headers.
DerivedArrayDataMatrixFileHeader
(col_no)[source]¶ DerivedArrayData header in an assay
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column_type
= 'Derived Array Data Matrix File'¶
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class
altamisa.isatab.headers.
DerivedDataFileHeader
(col_no)[source]¶ Derived Data File header in an assay
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column_type
= 'Derived Data File'¶
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class
altamisa.isatab.headers.
DerivedSpectralDataFileHeader
(col_no)[source]¶ DerivedSpectralData header in an assay
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column_type
= 'Derived Spectral Data File'¶
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class
altamisa.isatab.headers.
ImageFileHeader
(col_no)[source]¶ Image File header in an assay
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column_type
= 'Image File'¶
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class
altamisa.isatab.headers.
MetaboliteAssignmentFileHeader
(col_no)[source]¶ PeptideAssignment header in an assay
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column_type
= 'Metabolite Assignment File'¶
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class
altamisa.isatab.headers.
PeptideAssignmentFileHeader
(col_no)[source]¶ PeptideAssignment header in an assay
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column_type
= 'Peptide Assignment File'¶
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class
altamisa.isatab.headers.
PostTranslationalModificationAssignmentFileHeader
(col_no)[source]¶ PostTranslationalModificationAssignment header in an assay
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column_type
= 'Post Translational Modification Assignment File'¶
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class
altamisa.isatab.headers.
ProteinAssignmentFileHeader
(col_no)[source]¶ ProteinAssignment header in an assay
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column_type
= 'Protein Assignment File'¶
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class
altamisa.isatab.headers.
RawDataFileHeader
(col_no)[source]¶ Raw Data header in an assay
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column_type
= 'Raw Data File'¶
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class
altamisa.isatab.headers.
RawSpectralDataFileHeader
(col_no)[source]¶ Raw Spectral Data header in an assay
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column_type
= 'Raw Spectral Data File'¶
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class
altamisa.isatab.headers.
SpotPickingFileHeader
(col_no)[source]¶ SpotPickingFile header in an assay
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column_type
= 'Spot Picking File'¶
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class
altamisa.isatab.headers.
AssayNameHeader
(col_no)[source]¶ Assay Name header in an assay
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column_type
= 'Assay Name'¶
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class
altamisa.isatab.headers.
DataTransformationNameHeader
(col_no)[source]¶ DataTransformationName header in an assay
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column_type
= 'Data Transformation Name'¶
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class
altamisa.isatab.headers.
GelElectrophoresisAssayNameHeader
(col_no)[source]¶ GelElectrophoresisAssayName header in an assay
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column_type
= 'Gel Electrophoresis Assay Name'¶
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class
altamisa.isatab.headers.
HybridizationAssayNameHeader
(col_no)[source]¶ HybridizationAssayName header in an assay
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column_type
= 'Hybridization Assay Name'¶
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class
altamisa.isatab.headers.
MsAssayNameHeader
(col_no)[source]¶ MsAssayName header in an assay
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column_type
= 'MS Assay Name'¶
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class
altamisa.isatab.headers.
NormalizationNameHeader
(col_no)[source]¶ Normalization Name header in a assay
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column_type
= 'Normalization Name'¶
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class
altamisa.isatab.headers.
ProtocolRefHeader
(col_no)[source]¶ Protocol REF header in a study or assay
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column_type
= 'Protocol REF'¶
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class
altamisa.isatab.headers.
ScanNameHeader
(col_no)[source]¶ ScanName header in assay
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column_type
= 'Scan Name'¶
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class
altamisa.isatab.headers.
ArrayDesignRefHeader
(col_no)[source]¶ ArrayDesignRef header in an assay
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column_type
= 'Array Design REF'¶
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class
altamisa.isatab.headers.
DateHeader
(col_no)[source]¶ Date annotation header in a study or assay
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column_type
= 'Date'¶
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class
altamisa.isatab.headers.
FirstDimensionHeader
(col_no)[source]¶ First Dimension header in an assay
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column_type
= 'First Dimension'¶
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class
altamisa.isatab.headers.
LabelHeader
(col_no)[source]¶ Label header in an assay
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column_type
= 'Label'¶
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class
altamisa.isatab.headers.
MaterialTypeHeader
(col_no)[source]¶ Material Type header in an assay
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column_type
= 'Material Type'¶
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class
altamisa.isatab.headers.
PerformerHeader
(col_no)[source]¶ Performer header in an assay
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column_type
= 'Performer'¶
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class
altamisa.isatab.headers.
SecondDimensionHeader
(col_no)[source]¶ Second Dimension header in an assay
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column_type
= 'Second Dimension'¶
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class
altamisa.isatab.headers.
TermRefAnnotationHeader
(col_no)[source]¶ Term reference annotation header
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class
altamisa.isatab.headers.
UnitHeader
(col_no)[source]¶ Unit annotation header in a study or assay
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column_type
= 'Unit'¶
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class
altamisa.isatab.headers.
LabeledColumnHeader
(col_no, label)[source]¶ Base class for labeled column headers.
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column_type
= None¶ The value to use for the
type
argument.
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class
altamisa.isatab.headers.
CharacteristicsHeader
(col_no, label)[source]¶ Material
Characteristics[*]
header in a study or assay-
column_type
= 'Characteristics'¶
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class
altamisa.isatab.headers.
CommentHeader
(col_no, label)[source]¶ Comment
header in a study or assay-
column_type
= 'Comment'¶
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class
altamisa.isatab.headers.
FactorValueHeader
(col_no, label)[source]¶ Factor Value[*]
header in a study or assay-
column_type
= 'Factor Value'¶
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class
altamisa.isatab.headers.
ParameterValueHeader
(col_no, label)[source]¶ Protocol
Parameter Value[*]
header in a study or assay-
column_type
= 'Parameter Value'¶
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class
altamisa.isatab.headers.
HeaderParserBase
(tokens)[source]¶ Helper base class for parsing a header from a study or assay file.
Parameters: tokens (list) – List of strings, e.g. a split line read from a tsv/cvs file. -
allowed_headers
= None¶ Names of the allowed headers
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simple_headers
= {'Array Data File': <class 'altamisa.isatab.headers.ArrayDataFileHeader'>, 'Array Data Matrix File': <class 'altamisa.isatab.headers.ArrayDataMatrixFileHeader'>, 'Array Design File': <class 'altamisa.isatab.headers.ArrayDesignFileHeader'>, 'Array Design REF': <class 'altamisa.isatab.headers.ArrayDesignRefHeader'>, 'Assay Name': <class 'altamisa.isatab.headers.AssayNameHeader'>, 'Data Transformation Name': <class 'altamisa.isatab.headers.DataTransformationNameHeader'>, 'Date': <class 'altamisa.isatab.headers.DateHeader'>, 'Derived Array Data File': <class 'altamisa.isatab.headers.DerivedArrayDataFileHeader'>, 'Derived Array Data Matrix File': <class 'altamisa.isatab.headers.DerivedArrayDataMatrixFileHeader'>, 'Derived Data File': <class 'altamisa.isatab.headers.DerivedDataFileHeader'>, 'Derived Spectral Data File': <class 'altamisa.isatab.headers.DerivedSpectralDataFileHeader'>, 'Extract Name': <class 'altamisa.isatab.headers.ExtractHeader'>, 'First Dimension': <class 'altamisa.isatab.headers.FirstDimensionHeader'>, 'Gel Electrophoresis Assay Name': <class 'altamisa.isatab.headers.GelElectrophoresisAssayNameHeader'>, 'Hybridization Assay Name': <class 'altamisa.isatab.headers.HybridizationAssayNameHeader'>, 'Image File': <class 'altamisa.isatab.headers.ImageFileHeader'>, 'Label': <class 'altamisa.isatab.headers.LabelHeader'>, 'Labeled Extract Name': <class 'altamisa.isatab.headers.LabeledExtractHeader'>, 'Library Name': <class 'altamisa.isatab.headers.LibraryHeader'>, 'MS Assay Name': <class 'altamisa.isatab.headers.MsAssayNameHeader'>, 'Material Type': <class 'altamisa.isatab.headers.MaterialTypeHeader'>, 'Metabolite Assignment File': <class 'altamisa.isatab.headers.MetaboliteAssignmentFileHeader'>, 'Normalization Name': <class 'altamisa.isatab.headers.NormalizationNameHeader'>, 'Peptide Assignment File': <class 'altamisa.isatab.headers.PeptideAssignmentFileHeader'>, 'Performer': <class 'altamisa.isatab.headers.PerformerHeader'>, 'Post Translational Modification Assignment File': <class 'altamisa.isatab.headers.PostTranslationalModificationAssignmentFileHeader'>, 'Protein Assignment File': <class 'altamisa.isatab.headers.ProteinAssignmentFileHeader'>, 'Protocol REF': <class 'altamisa.isatab.headers.ProtocolRefHeader'>, 'Raw Data File': <class 'altamisa.isatab.headers.RawDataFileHeader'>, 'Raw Spectral Data File': <class 'altamisa.isatab.headers.RawSpectralDataFileHeader'>, 'Sample Name': <class 'altamisa.isatab.headers.SampleHeader'>, 'Scan Name': <class 'altamisa.isatab.headers.ScanNameHeader'>, 'Second Dimension': <class 'altamisa.isatab.headers.SecondDimensionHeader'>, 'Source Name': <class 'altamisa.isatab.headers.SourceHeader'>, 'Spot Picking File': <class 'altamisa.isatab.headers.SpotPickingFileHeader'>, 'Unit': <class 'altamisa.isatab.headers.UnitHeader'>}¶ Headers that are mapped to
SimpleColumnHeader
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labeled_headers
= {'Characteristics': <class 'altamisa.isatab.headers.CharacteristicsHeader'>, 'Comment': <class 'altamisa.isatab.headers.CommentHeader'>, 'Factor Value': <class 'altamisa.isatab.headers.FactorValueHeader'>, 'Parameter Value': <class 'altamisa.isatab.headers.ParameterValueHeader'>}¶ Labeled headers
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class
altamisa.isatab.headers.
StudyHeaderParser
(tokens)[source]¶ Helper class for parsing header of a study or assay.
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file_type
= 'study'¶
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allowed_headers
= ('Sample Name', 'Source Name', 'Protocol REF', 'Date', 'Performer', 'Characteristics', 'Comment', 'Factor Value', 'Parameter Value', 'Term Source REF', 'Unit')¶
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class
altamisa.isatab.headers.
AssayHeaderParser
(tokens)[source]¶ Helper class for parsing header of a assay file.
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file_type
= 'assay'¶
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allowed_headers
= ('Extract Name', 'Labeled Extract Name', 'Library Name', 'Sample Name', 'Array Data File', 'Array Data Matrix File', 'Array Design File', 'Derived Array Data File', 'Derived Array Data Matrix File', 'Derived Data File', 'Derived Spectral Data File', 'Image File', 'Metabolite Assignment File', 'Peptide Assignment File', 'Post Translational Modification Assignment File', 'Protein Assignment File', 'Raw Data File', 'Raw Spectral Data File', 'Spot Picking File', 'Assay Name', 'Data Transformation Name', 'Gel Electrophoresis Assay Name', 'Hybridization Assay Name', 'MS Assay Name', 'Normalization Name', 'Protocol REF', 'Scan Name', 'Array Design REF', 'Date', 'First Dimension', 'Label', 'Material Type', 'Performer', 'Second Dimension', 'Characteristics', 'Comment', 'Parameter Value', 'Term Source REF', 'Unit')¶
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