bioitem append

bioitem append bhandle label ?property value?...

i.append({?property:value,?...})

i.append(?property,value,?...)

Standard data manipulation command for appending property data. It is explained in more detail in the section about setting property data.

The command returns the first data value.

bioitem defined

bioitem defined bhandle label property

i.defined(property)

This command checks whether a property is defined for the bioitem. This is explained in more detail in the section about property validity checking. Note that this is not a check for the presence of property data! The biologics valid command is used for this purpose.

The command returns a boolean status value.

bioitem delete

bioitem delete bhandle ?label?...

bioitem delete bhandle all

i.delete()

Bioitem.Delete(eref,?ilabel/iref/irefsequence?,...)

Biooitem.Delete(iref,...)

Bioitem.Delete(bref,“all”)

Delete zero or more bioitems. All biolinks which the bioitems participate in are also deleted.

The special bioitem label all requests deletion of all bioitems.

The return value of the command is the number of deleted bioitems.

Example:

bioitem delete $bhandle 1

This command is one of few bioitem subcommands which do not require an bioitem label. If no label is given, the command does nothing. This is useful for list expansions where the list might be empty:

eval bioitem delete $bhandle $delitemlist

bioitem delete $bhandle {*}$delitemlist

bioitem dget

bioitem dget bhandle label propertylist ?filterset? ?parameterdict?

i.dget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the bioitem get command. The difference between bioitem get and bioitem dget is that the latter does not attempt computation of property data, but rather initializes the property values to the default and return that default if the data is not yet available. For data already present, biooitem get and bioitem dget are equivalent.

bioitem exists

bioitem exists bhandle label ?filterlist?

i.exists(?filters=?)

Bioitem.Exists(bref,label,?filters=?)

Check whether this bioitem exists. Optionally, a filter list can be supplied to check for the presence of specific features. The command returns 0 if the bioitem does not exist, or fails the filter, and 1 in case of successful testing.

Example:

bioitem exists $bhandle 99

bioitem fill

bioitem fill bhandle label ?property value?...

i.fill({property:value,...})

i.fill(?property,value?,...)

Standard data manipulation command for setting data, ignoring possible mismatches between the lengths of the lists of objects associated with the property and the value list. It is explained in more detail in the section about setting property data.

bioitem filter

bioitem filter bhandle label filterlist

i.filter(filters)

Check whether a bioitem passes a filter list. The return value is boolean 1 for success and 0 for failure.

bioitem get

bioitem get bhandle label propertylist ?filterset? ?parameterdict?

i.get(property=,?filters=?,?parameters=?)

i[property]

i.property

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For the use of the optional property parameter list argument, refer to the documentation of the ens get command.

Variants of the bioitem get command are bioitem new, bioitem dget, bioitem nget, bioitem show, bioitem sqldget , bioitem sqlget, bioitem sqlnew and bioitem sqlshow.

bioitem index

bioitem index bhandle label

i.index()

Get the index of the bioitem. The index is the position in the bioitem list of the biologics object. The first position is index 0.

bioitem jget

bioitem jget bhandle label propertylist ?filterset? ?parameterdict?

i.jget(property=,?filters=?,?parameters=?)

This is a variant of bioitem get which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

bioitem jnew

bioitem jnew bhandle label propertylist ?filterset? ?parameterdict?

i.jnew(property=,?filters=?,?parameters=?)

This is a variant of bioitem new which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

bioitem jshow

bioitem jshow bhandle label propertylist ?filterset? ?parameterdict?

i.jshow(property=,?filters=?,?parameters=?)

This is a variant of bioitem show which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

bioitem item

bioitem item bhandle label

Bioitem.Ref(bref,identifier)

Return the bioitem label stored in property I_LABEL ( Tcl ) , or a minor object reference ( Python ). This is useful in case the label used in the command is not a straightforward numerical label or reference but some other item identification format.

bioitem bioitem is an alias.

bioitem links

bioitem links bhandle label ?filterset? ?filtermode?

i.links(?filters=?,?mode=?)

Standard cross-referencing command to obtain the labels or references of the biolinks which connect this bioitem fragment. This is explained in more detail in the section about object cross-references.

bioitem biolinks is a command alias.

bioitem new

bioitem new bhandle label propertylist ?filterset? ?parameterdict?

i.new(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the bioitem get command. The difference between bioitem get and bioitem new is that the latter forces the re-computation of the property data, regardless whether it is present and valid, or not.

bioitem nget

bioitem nget bhandle label propertylist ?filterset? ?parameterdict?

i.nget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the bioitem get command. The difference between bioitem get and bioitem nget is that the latter always returns numeric data, even if symbolic names for the values are available.

bioitem ref

Bioitem.Ref(bref,identifier)

Python only method to get a bioitem reference. See bioitem item command.

bioitem set

bioitem set bhandle label ?property value?...

i.set(?property,value?,...)

i.set({property:value,...})

i.property = value

i[property] = value

Standard data manipulation command. It is explained in more detail in the section about setting property data.

bioitem show

bioitem show bhandle label propertylist ?filterset? ?parameterdict?

i.show(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the bioitem get command. The difference between bioitem get and bioitem show is that the latter does not attempt computation of property data, but raises an error if the data is not present and valid. For data already present, bioitem get and bioitem show are equivalent.

bioitem sqldget

bioitem sqldget bhandle label propertylist ?filterset? ?parameterdict?

i.sqldget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the atom get command. The differences between bioitem get and bioitem sqldget are that the latter does not attempt computation of property data, but initializes the property value to the default and returns that default, if the data is not present and valid; and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

bioitem sqlget

bioitem sqlget bhandle label propertylist ?filterset? ?parameterdict?

i.sqlget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the bioitem get command. The difference between bioitem get and bioitem sqlget is that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

bioitem sqlnew

bioitem sqlnew bhandle label propertylist ?filterset? ?parameterdict?

i.sqlnew(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the bioitem get command. The differences between bioitem get and bioitem sqlnew are that the latter forces re-computation of the property data, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

bioitem sqlshow

bioitem sqlshow bhandle label propertylist ?filterset? ?parameterdict?

i.sqlshow(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the bioitem get command. The differences between bioitem get and bioitem sqlshow are that the latter does not attempt computation of property data, but raises an error if the data is not present and valid, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

bioitem subcommands

bioitem subcommands

dir(Bioitem)

Lists all subcommands of the bioitem command. Note that this command does not require a biologics handle, or a bioitem label.