Headers

This module contains code for the representation of headers from study and assay files and parsing thereof.

class altamisa.isatab.headers.ColumnHeader(column_type, col_no, span)

Column header in a study or assay file

column_type

The type of this header

col_no

The column number this header refers to

span

Number of columns this header spans

term_source_ref_header

Link to the TermSourceRefHeader to use

unit_header

Link to the UnitHeader to use

get_simple_string() → List[str]

Return a list of simple string representations of the column types

class altamisa.isatab.headers.SimpleColumnHeader(col_no)

Base class for simple column headers.

column_type = None

The value to use for the type argument.

class altamisa.isatab.headers.ExtractHeader(col_no)

Extract header in an assay

column_type = 'Extract Name'

The value to use for the type argument.

class altamisa.isatab.headers.LabeledExtractHeader(col_no)

Labeled Extract header in an assay

column_type = 'Labeled Extract Name'

The value to use for the type argument.

class altamisa.isatab.headers.LibraryHeader(col_no)

Library header in an assay

column_type = 'Library Name'

The value to use for the type argument.

class altamisa.isatab.headers.SampleHeader(col_no)

Sample header in a study or assay

column_type = 'Sample Name'

The value to use for the type argument.

class altamisa.isatab.headers.SourceHeader(col_no)

Source header in a study

column_type = 'Source Name'

The value to use for the type argument.

class altamisa.isatab.headers.ArrayDataFileHeader(col_no)

ArrayData header in an assay

column_type = 'Array Data File'

The value to use for the type argument.

class altamisa.isatab.headers.ArrayDataMatrixFileHeader(col_no)

ArrayData Matrix File header in an assay

column_type = 'Array Data Matrix File'

The value to use for the type argument.

class altamisa.isatab.headers.ArrayDesignFileHeader(col_no)

ArrayDesignFile header in an assay

column_type = 'Array Design File'

The value to use for the type argument.

class altamisa.isatab.headers.DerivedArrayDataFileHeader(col_no)

DerivedArrayData header in an assay

column_type = 'Derived Array Data File'

The value to use for the type argument.

class altamisa.isatab.headers.DerivedArrayDataMatrixFileHeader(col_no)

DerivedArrayData header in an assay

column_type = 'Derived Array Data Matrix File'

The value to use for the type argument.

class altamisa.isatab.headers.DerivedDataFileHeader(col_no)

Derived Data File header in an assay

column_type = 'Derived Data File'

The value to use for the type argument.

class altamisa.isatab.headers.DerivedSpectralDataFileHeader(col_no)

DerivedSpectralData header in an assay

column_type = 'Derived Spectral Data File'

The value to use for the type argument.

class altamisa.isatab.headers.ImageFileHeader(col_no)

Image File header in an assay

column_type = 'Image File'

The value to use for the type argument.

class altamisa.isatab.headers.MetaboliteAssignmentFileHeader(col_no)

PeptideAssignment header in an assay

column_type = 'Metabolite Assignment File'

The value to use for the type argument.

class altamisa.isatab.headers.PeptideAssignmentFileHeader(col_no)

PeptideAssignment header in an assay

column_type = 'Peptide Assignment File'

The value to use for the type argument.

class altamisa.isatab.headers.PostTranslationalModificationAssignmentFileHeader(col_no)

PostTranslationalModificationAssignment header in an assay

column_type = 'Post Translational Modification Assignment File'

The value to use for the type argument.

class altamisa.isatab.headers.ProteinAssignmentFileHeader(col_no)

ProteinAssignment header in an assay

column_type = 'Protein Assignment File'

The value to use for the type argument.

class altamisa.isatab.headers.RawDataFileHeader(col_no)

Raw Data header in an assay

column_type = 'Raw Data File'

The value to use for the type argument.

class altamisa.isatab.headers.RawSpectralDataFileHeader(col_no)

Raw Spectral Data header in an assay

column_type = 'Raw Spectral Data File'

The value to use for the type argument.

class altamisa.isatab.headers.SpotPickingFileHeader(col_no)

SpotPickingFile header in an assay

column_type = 'Spot Picking File'

The value to use for the type argument.

class altamisa.isatab.headers.AssayNameHeader(col_no)

Assay Name header in an assay

column_type = 'Assay Name'

The value to use for the type argument.

class altamisa.isatab.headers.DataTransformationNameHeader(col_no)

DataTransformationName header in an assay

column_type = 'Data Transformation Name'

The value to use for the type argument.

class altamisa.isatab.headers.GelElectrophoresisAssayNameHeader(col_no)

GelElectrophoresisAssayName header in an assay

column_type = 'Gel Electrophoresis Assay Name'

The value to use for the type argument.

class altamisa.isatab.headers.HybridizationAssayNameHeader(col_no)

HybridizationAssayName header in an assay

column_type = 'Hybridization Assay Name'

The value to use for the type argument.

class altamisa.isatab.headers.MsAssayNameHeader(col_no)

MsAssayName header in an assay

column_type = 'MS Assay Name'

The value to use for the type argument.

class altamisa.isatab.headers.NormalizationNameHeader(col_no)

Normalization Name header in a assay

column_type = 'Normalization Name'

The value to use for the type argument.

class altamisa.isatab.headers.ProtocolRefHeader(col_no)

Protocol REF header in a study or assay

column_type = 'Protocol REF'

The value to use for the type argument.

class altamisa.isatab.headers.ScanNameHeader(col_no)

ScanName header in assay

column_type = 'Scan Name'

The value to use for the type argument.

class altamisa.isatab.headers.ArrayDesignRefHeader(col_no)

ArrayDesignRef header in an assay

column_type = 'Array Design REF'

The value to use for the type argument.

class altamisa.isatab.headers.DateHeader(col_no)

Date annotation header in a study or assay

column_type = 'Date'

The value to use for the type argument.

class altamisa.isatab.headers.FirstDimensionHeader(col_no)

First Dimension header in an assay

column_type = 'First Dimension'

The value to use for the type argument.

class altamisa.isatab.headers.LabelHeader(col_no)

Label header in an assay

column_type = 'Label'

The value to use for the type argument.

class altamisa.isatab.headers.MaterialTypeHeader(col_no)

Material Type header in an assay

column_type = 'Material Type'

The value to use for the type argument.

class altamisa.isatab.headers.PerformerHeader(col_no)

Performer header in an assay

column_type = 'Performer'

The value to use for the type argument.

class altamisa.isatab.headers.SecondDimensionHeader(col_no)

Second Dimension header in an assay

column_type = 'Second Dimension'

The value to use for the type argument.

class altamisa.isatab.headers.TermRefAnnotationHeader(col_no)

Term reference annotation header

get_simple_string() → List[str]

Return a list of simple string representations of the column types

class altamisa.isatab.headers.UnitHeader(col_no)

Unit annotation header in a study or assay

column_type = 'Unit'

The value to use for the type argument.

class altamisa.isatab.headers.LabeledColumnHeader(col_no, label)

Base class for labeled column headers.

column_type = None

The value to use for the type argument.

get_simple_string()

Return a list of simple string representations of the column types

class altamisa.isatab.headers.CharacteristicsHeader(col_no, label)

Material Characteristics[*] header in a study or assay

column_type = 'Characteristics'

The value to use for the type argument.

class altamisa.isatab.headers.CommentHeader(col_no, label)

Comment header in a study or assay

column_type = 'Comment'

The value to use for the type argument.

class altamisa.isatab.headers.FactorValueHeader(col_no, label)

Factor Value[*] header in a study or assay

column_type = 'Factor Value'

The value to use for the type argument.

class altamisa.isatab.headers.ParameterValueHeader(col_no, label)

Protocol Parameter Value[*] header in a study or assay

column_type = 'Parameter Value'

The value to use for the type argument.

class altamisa.isatab.headers.HeaderParserBase(tokens)

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

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

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

run() → Iterator[ColumnHeader]

Parse the header

class altamisa.isatab.headers.StudyHeaderParser(tokens)

Helper class for parsing header of a study or assay.

allowed_headers = ('Sample Name', 'Source Name', 'Protocol REF', 'Date', 'Performer', 'Characteristics', 'Comment', 'Factor Value', 'Parameter Value', 'Term Source REF', 'Unit')

Names of the allowed headers

class altamisa.isatab.headers.AssayHeaderParser(tokens)

Helper class for parsing header of a assay file.

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')

Names of the allowed headers