sfftk.notes package

Find notes

sfftk.notes.find

Search for terms and display ontologies

class sfftk.notes.find.CSVRow(row_data, fields, index, *args, **kwargs)[source]

Bases: Table

Class definition for a single row in the table

class sfftk.notes.find.CSVTable(search_results, fields, width='auto', *args, **kwargs)[source]

Bases: Table

Class that formats search results as a CSV

class sfftk.notes.find.ResultsTable(search_results, fields, width='auto', *args, **kwargs)[source]

Bases: Table

Class that formats search results as a table

class sfftk.notes.find.SearchResource(args, configs)[source]

Bases: object

A resource against which to look for accessions or terms

get_url()[source]

Determine the url to search against

search(*args, **kwargs)[source]

Perform a search against this resource

class sfftk.notes.find.SearchResults(resource, as_text=False)[source]

Bases: object

SearchResults class

tabulate(as_text=False)[source]

Tabulate the search results

class sfftk.notes.find.Table[source]

Bases: object

Table superclass

class sfftk.notes.find.TableField(name, key=None, text=None, width=20, pc=None, justify='left', _format=None, is_index=False, is_iterable=False, position_in_iterable=0)[source]

Bases: object

Class definition for a TableField - single column in a table

property is_index

Is this field an index (numbered) field?

justify(text)[source]

Justify the given text

Parameters:

text (str) – the text to justify

property pc

The width of the field in percent; resolves to a character width

render(row_data, index)[source]

Render this field

property width

The width of the field in characters

class sfftk.notes.find.TableRow(row_data, fields, index, *args, **kwargs)[source]

Bases: Table

Class definition for a single row in the table

Wrapping is automatically handled

View notes

sfftk.notes.view

Display notes in EMDB-SFF files

class sfftk.notes.view.HeaderView(segmentation)[source]

Bases: View

HeaderView class

Display EMDB-SFF header

class sfftk.notes.view.NoteView(segment, _long=False, list_ids=False)[source]

Bases: View

NoteView class

Display annotation for a single segment

class sfftk.notes.view.TableHeaderView[source]

Bases: View

Class defining the view of a table header object

class sfftk.notes.view.View[source]

Bases: object

View base class

sfftk.notes.view.list_notes(args, configs)[source]

List all notes in an EMDB-SFF file

Parameters:

args (argparse.Namespace) – parsed arguments

Return status:

0 is OK, else failure

Rtype status:

int

sfftk.notes.view.show_notes(args, configs)[source]

Show notes in an EMDB-SFF file for the specified segment IDs

Parameters:

args (argparse.Namespace) – parsed arguments

Return status:

0 is OK, else failure

Rtype status:

int

Modify notes

sfftk.notes.modify

Add, edit and delete terms in EMDB-SFF files

class sfftk.notes.modify.AbstractGlobalNote[source]

Bases: BaseNote

Abstract class definition for global annotations which defines attributes of global annotation.

Also defines three methods that effect the annotation to a segmentation object:

add_to_segmentation(segmentation)[source]

Adds this note to the given segmentation

Parameters:

segmentation (sfftkrw.SFFSegmentation) – an EMDB-SFF segmentation object

Return segmentation:

the EMDB-SFF segmentation with the annotation added

del_from_segmentation(segmentation)[source]

Delete attributes from a segmentation

Parameters:

segmentation (sfftkrw.SFFSegmentation) – an EMDB-SFF segmentation object

Return segmentation:

the EMDB-SFF segmentation with annotation deleted

Rtype segmentation:

sfftkrw.SFFSegmentation

edit_in_segmentation(segmentation)[source]

Modify the global annotation of the given segmentation

Parameters:

segmentation (sfftkrw.SFFSegmentation) – an EMDB-SFF segmentation object

Return segmentation:

the EMDB-SFF segmentation with annotated edited

Rtype segmentation:

sfftkrw.SFFSegmentation

class sfftk.notes.modify.AbstractNote[source]

Bases: BaseNote

Note ‘abstact’ class that defines private attributes and main methods

add_to_segment(segment)[source]

Add the annotations found in this Note object to the sfftkrw.SFFSegment object

Parameters:

segment (sfftkrw.SFFSegment) – single segment in EMDB-SFF

del_from_segment(segment)[source]

Delete the annotations found in this Note object to the sfftkrw.SFFSegment object

Parameters:

segment (sfftkrw.SFFSegment) – single segment in EMDB-SFF

edit_in_segment(segment)[source]

Edit the annotations found in this Note object to the sfftkrw.SFFSegment object

Parameters:

segment (sfftkrw.SFFSegment) – single segment in EMDB-SFF

class sfftk.notes.modify.ArgsNote(args, configs, *args_, **kwargs_)[source]

Bases: AbstractNote

Class definition for an ArgsNote object

class sfftk.notes.modify.BaseNote[source]

Bases: object

Note base class

class sfftk.notes.modify.ExternalReference(resource=None, url=None, accession=None)[source]

Bases: object

Class definition for a ExternalReference object

property iri

The IRI value should be double url-encoded

class sfftk.notes.modify.GlobalArgsNote(args, configs, *args_, **kwargs_)[source]

Bases: AbstractGlobalNote

Class defining segmentation (global) annotation based on command-line arguments

Parameters:
class sfftk.notes.modify.GlobalSimpleNote(name=None, software_id=None, software_name=None, software_version=None, software_processing_details=None, transform_id=None, transform=None, details=None, external_reference_id=None, external_references=None, *args, **kwargs)[source]

Bases: AbstractGlobalNote

Class definition for global segmentation notes

class sfftk.notes.modify.NoteAttr(initval=None, name='var')[source]

Bases: object

Descriptor class for note attributes

Parameters:

  • initval – the initial value of the attribute (default: None)

  • name (str) – the name of the variable (default: ‘var’)

class sfftk.notes.modify.SimpleNote(name=None, description=None, number_of_instances=None, external_reference_id=None, external_references=None, *args, **kwargs)[source]

Bases: AbstractNote

Class definition for a SimpleNote object

sfftk.notes.modify.add_note(args, configs)[source]

Add annotation to a segment specified in args

Parameters:
Return status:

status

Rtype status:

int

sfftk.notes.modify.clear_notes(args, configs)[source]

Clear notes from segments

Parameters:
Return status:

status

Rtype status:

int

sfftk.notes.modify.copy_notes(args, configs)[source]

Copy notes across segments

One or more segments can be chosen for either or both source and destination

Parameters:
Return status:

status

Rtype status:

int

sfftk.notes.modify.del_note(args, configs)[source]

Delete annotation to a segment specified in args

Parameters:
Return status:

status

Rtype status:

int

sfftk.notes.modify.edit_note(args, configs)[source]

Edit annotation to a segment specified in args

Parameters:
Return status:

status

Rtype status:

int

sfftk.notes.modify.merge(args, configs)[source]

Merge notes from two EMDB-SFF files

Parameters:
Return status:

status

Rtype status:

int

sfftk.notes.modify.save(args, configs)[source]

Save changes made

Parameters:
Return status:

status

Rtype status:

int

sfftk.notes.modify.trash(args, configs)[source]

Trash changes made

Parameters:
Return status:

status

Rtype status:

int