remove <entity type> <other arguments>

    The 'remove' command is used to remove entities.  The type of entity to

    remove is determined by the '<entity type>' argument.  The '<other

    arguments>' are determined by the entity type.  For project records, the

    '<other arguments>' is generally the name of the record to remove.

    The following entities are available for removing.  Run

    'help remove <entity type>' for more detailed information.

    amplicon        Removes an amplicon from the currently open project.

    mid             Removes an MID from the currently open project.

    midGroup        Removes an MID group from the currently open project.

    multiplexer     Removes a multiplexer from the currently open project.

    readData        Removes a read data from the currently open project.

    readGroup       Removes a read group from the currently open project.

    reference       Removes a reference sequence from the currently open

                        project.

    sample          Removes a sample from the currently open project.

    variant         Removes a variant from the currently open project.

    remove amp[licon] <amplicon name> [-ofRef <reference sequence name>]

                                      [-file <file> [-format <format>]]

    remove amp[licon] -name <amplicon name>

                      [-ofRef <reference sequence name>]

                      [-file <file> [-format <format>]]

    Removes an amplicon.  In the first form, the non-option argument is used as

    the name of the amplicon to remove.  In the second, a name must be

    explicitly specified in option form.  

    Amplicons are allowed to have duplicate names as long as the reference

    sequences to which they refer are distinct.  The '-ofRef' argument can be

    used to refer to such amplicons.  For example, if we have two amplicons

    named "MyAmp", but one of them refers to "ReferenceSequence1" and the other

    to "ReferenceSequence2", we can use the '-ofRef' option to distinguish

    them.  We can run 'remove amplicon "MyAmp" -ofRef "ReferenceSequence1"' to

    remove the former amplicon.

    If the amplicon name is given as the character '*' then all amplicons will

    be removed.  If the '-ofRef' option is also supplied, then all the 

    amplicons of just that reference sequence will be removed.

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove mid <mid name> [-ofMidGroup <midGroup>]

                          [-file <file> [-format <format>]]

    remove mid -name <mid name>

               [-ofMidGroup <midGroup>]

               [-file <file> [-format <format>]]

    Removes an MID.  In the first form, the non-option argument is used as

    the name of the MID to remove.  In the second, a name must be

    explicitly specified in option form.  

    MIDs are allowed to have duplicate names as long as they belong to

    distinct MID groups.  The '-ofMidGroup' argument can be used to refer to

    such MIDs.  For example, if we have two MIDs named "MyMID", but one of

    them is a member of MID group "MID_Group1" and the other is a member of

    MID group "MID_Group2", we can use the '-ofMidGroup' option to distinguish

    them.  We can run 'remove mid "MyMID" -ofMidGroup "MID_Group1"' to remove

    the former MID.

    If the MID name is given as the character '*' then all MIDs will

    be removed.  If the '-ofMidGroup' option is also supplied, then all the 

    MIDs of just that MID group will be removed.

    Removing MIDs also results in the removal of any associations in which

    they are participants.

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove midGroup <read group name> [-file <file> [-format <format>]]

    remove midGroup -name <read group name> [-file <file> [-format <format>]]

    Removes an MID group.  In the first form, the non-option argument is used

    as the name of the read group to remove.  In the second, a name must be

    explicitly specified in option form.

    If an MID group is removed, then all the MIDs of that group are

    also removed. 

    If the MID group name is given as the character '*' then all MID groups

    will be removed.  This would remove all the MIDs that belong to MID groups

    from the project at the same time, but it would leave behind any MIDs that

    do not have an MID group assignment.

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove mul[tiplexer] <multiplexer name> [-file <file> [-format <format>]]

    remove mul[tiplexer] -name <multiplexer name> 

                         [-file <file> [-format <format>]]

    Removes a multiplexer.  In the first form, the non-option argument

    is used as the name of the multiplexer to remove.  In the second, a

    name must be explicitly specified in option form.  

    If a multiplexer is removed, then all the associations that include that 

    multiplexer (such as multiplexer-readData and multiplexer-MID associations)

    are removed at the same time.

    If the multiplexer name is given as the character '*' then all the 

    multiplexers will be removed along with the associations in which they 

    participate.

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove readData <read data name> [-file <file> [-format <format>]]

    remove readData -name <read data name> [-file <file> [-format <format>]]

    Removes a read data.  In the first form, the non-option argument is used as

    the name of the read data to remove.  In the second, a name must be

    explicitly specified in option form. 

    If the read data name is given as the character '*' then all read

    data will be removed. 

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove readGroup <read group name> [-file <file> [-format <format>]]

    remove readGroup -name <read group name> [-file <file> [-format <format>]]

    Removes a read group.  In the first form, the non-option argument is used

    as the name of the read group to remove.  In the second, a name must be

    explicitly specified in option form.

    If a read group is removed, then all the read data of that group are

    also removed. 

    If the read group name is given as the character '*' then all read groups

    will be removed.  This would effectively remove all the read data from

    the project at the same time.

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove ref[erence] <reference name> [-file <file> [-format <format>]]

    remove ref[erence] -name <reference name> [-file <file> [-format <format>]]

    Removes a reference sequence.  In the first form, the non-option argument

    is used as the name of the reference sequence to remove.  In the second, a

    name must be explicitly specified in option form.  

    If a reference sequence is removed, then all the amplicons and variants

    associated with that reference sequence are removed at the same time.

    If the reference sequence name is given as the character '*' then all

    the reference sequences will be removed.  This would effectively remove

    all the amplicons and variants at the same time.

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove sam[ple] <sample name> [-file <file> [-format <format>]]

    remove sam[ple] -name <sample name> [-file <file> [-format <format>]]

    Removes a sample.  In the first form, the non-option argument is used as

    the name of the sample to remove.  In the second, a name must be explicitly

    specified in option form.  

    If the sample name is given as the character '*' then all samples will be

    removed.

    Run 'help general tabularCommands' for information about the '-file'

    option.

    remove var[iant] <variant name> [-ofRef <reference sequence name>]

                                    [-file <file> [-format <format>]]

    remove var[iant] -name <variant name>

                     [-ofRef <reference sequence name>]

                     [-file <file> [-format <format>]]

    Removes a variant.  In the first form, the non-option argument is used as

    the name of the variant to remove.  In the second, a name must be

    explicitly specified in option form.  

    Variants are allowed to have duplicate names as long as the reference

    sequences to which they refer are distinct.  The '-ofRef' argument can be

    used to refer to such variants.  For example, if we have two variants named

    "MyVar", but one of them refers to "ReferenceSequence1" and the other to

    "ReferenceSequence2", we can use the '-ofRef' option to distinguish them.

    We can run 'remove amplicon "MyVar" -ofRef "ReferenceSequence1"' to remove

    the former variant.

    If the variant name is given as the character '*' then all variants will

    be removed.  If the '-ofRef' option is also supplied, then all the variants

    of just that reference sequence will be removed.

    Run 'help general tabularCommands' for information about the '-file'

    option.

© 2011 454 Life Sciences Corporation, a Roche Company.

For life science research only. Not for use in diagnostic procedures.