update <entity type> <other arguments>

    The 'update' command is used to update properties of entities.  For

    example, you can update the annotation of an amplicon by running, 

    'update amplicon "My Amplicon" -annotation "New annotation"'.

    The following entities are available for updating.  Run

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

    amplicon        Updates an amplicon in the currently open project.

    mid             Updates an MID in the currently open project.

    midGroup        Updates an MID group in the currently open project.

    multiplexer     Updates a multiplexer in the currently open project.

    project         Updates the currently open project.

    readData        Updates a read data in the currently open project.

    readGroup       Updates a read group in the currently open project.

    reference       Updates a reference sequence in the currently open project.

    sample          Updates a sample in the currently open project.

    variant         Updates a variant in the currently open project.

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

                                          [-annot[ation] <annotation>]

                                          [-ref[erence] <reference name>]

                                          [-primer1 <primer 1 sequence>]

                                          [-primer2 <primer 2 sequence>]

                                          [-start <target start index>]

                                          [-end <target end index>]

                                          [-checkPri[merMatch] <boolean>]

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

    update amp[licon] -name <new amplicon name>

                      [-ofRef <reference sequence name>]

                      [-annot[ation] <annotation>]

                      [-ref[erence] <reference name>]

                      [-primer1 <primer 1 sequence>]

                      [-primer2 <primer 2 sequence>]

                      [-start <target start index>]

                      [-end <target end index>]

                      [-checkPri[merMatch] <boolean>]

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

    Updates an amplicon in the currently open project.  In the first form, the

    non-option argument is used as the name of the amplicon to update.  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 'update amplicon "MyAmp" -ofRef "ReferenceSequence1"' to update

    the former amplicon.

    The remainder of the options are not required but are used to set

    properties of the amplicon.

        -ofRef              The name of the reference sequence to which the

                                amplicon currently refers to help disambiguate

                                amplicons with the same name.

        -annotation         The annotation.

        -reference          The name of the reference sequence with which to

                                associate the amplicon.

        -primer1            The primer 1 sequence.  This must be a nucleotide

                                sequence string conforming to IUPAC

                                nomenclature.  Any ambiguous symbols are

                                considered 'N's.

        -primer2            The primer 2 sequence.  This must be a nucleotide

                                sequence string conforming to IUPAC

                                nomenclature.  Any ambiguous symbols are

                                considered 'N's.

        -start              The index of the target start position, or a '*'

                                to indicate the position should be

                                automatically assigned.

        -end                The index of the target end position, or a '*'     

                                to indicate the position should be

                                automatically assigned.

        -checkPrimerMatch   Whether the system should check for a match between

                                the reference sequence and the primers in the

                                bases flanking the target region.  This must be

                                'true' or 'false', and defaults to 'true'.

    The start and end options indicate the positional range of the amplified

    target as measured from the first base of the associated reference

    sequence.  In the case that the primer sequences are included in the

    reference sequence, the system can automatically assign these positions by

    finding matches of primer1 and the reverse complement of primer2 and

    assigning the start and end positions to be just inside these matches.

    Either, or both, of the start and end positions may be specified as a '*'

    to request this search.  If one position is provided and the other is a

    '*', then one position will be constrained as given and the search will

    proceed on the other position.  If no such matching pair, or more than one

    matching pair can be found, then an error is generated.  N's in either the

    reference or primer sequences count as matches, but any match that involves

    greater than 50% N's will be rejected.  Any other substitutions,

    insertions, or deletions are not permitted.  Using a '*' for either the

    start or end implies the checkPrimerMatch option and requires exact matches

    of both primers in the reference sequence.  If the primers are not included

    in the reference or if the primers contain bases that don't exactly match

    the reference, the checkPrimerMatch option should be specified as 'false'

    to prevent an error from being generated, and both start and end positions

    should be explicitly provided.

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

    option.

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

                          [-seq[uence] <sequence>]

                          [-annot[ation] <annotation>]

                          [-midGroup <midGroup>]

                          [-checkMidGroup <boolean>]

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

    update mid -name <mid name> 

               [-ofMidGroup <midGroup>]

               [-seq[uence] <sequence>]

               [-annot[ation] <annotation>]

               [-midGroup <midGroup>]

               [-checkMidGroup <boolean>]

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

    Updates an MID in the currently open project.  In the first form,

    the non-option argument is used as the name of the MID to update.  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 'update mid "MyMID" -ofMidGroup "MID_Group1"' to update the former 

    MID.   

    The remainder of the options are not required but can be used to set 

    properties of the MID.

        -annotation         The annotation.

        -sequence           The MID sequence.  This must be a non-zero length 

                                nucleotide sequence string containing only the 

                                bases A, C, T and G.

        -midGroup           The MID group of the MID if it belongs to a group. 

                                This must be a pre-existing group such as one 

                                created using the 'create midGroup' command. 

        -checkMidGroup      Whether the system should check for compatibility

                                between the new MID sequence and other pre-

                                existing MID sequences belonging to the same 

                                MID group.  This must be 'true' or 'false', 

                                and defaults to 'true'.

    The name of the MID must be unique within the MID group it belongs to 

    (or unique within the project if the MID is not assigned to an MID group).

    The rules for '-checkMidGroup' compatibility are as follows:

    - An MID with an undefined sequence is considered compatible with any MID 

      group, under the assumption that its compatibility will eventually be

      assessed when a defined sequence gets assigned to the MID.

    - An MID with a defined sequence must have the same length as other

      defined MID sequences within an MID group to be compatible with the

      group. If the new MID sequence is the first defined sequence added to

      the MID group, the required sequence length for subsequent MIDs of the

      group with be the length of that first defined MID sequence.

    - An MID with a defined sequence must not be identical (ignoring case) 

      with any other defined, pre-existing MID sequence of the same MID group.

    If it becomes necessary to edit existing MIDs in a way that temporarily 

    leaves the MIDs in a group in an inconsistent state (such as changing the 

    lengths of sequences in an MID group), '-checkMidGroup' should be set to 

    'false'. 

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

    option.

    update midGroup <midGroup name> [-annot[ation] <annotation>]

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

    update midGroup -name <midGroup name> 

                    [-annot[ation] <annotation>]

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

    Updates an MID group in the currently open project.  In the first form,

    the non-option argument is used as the name of the MID group to update.  

    In the second, a name must be explicitly specified in option form.  The 

    remainder of the options are not required but can be used to set

    properties of the MID group.

        -annotation     The annotation.

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

    option.

    update mul[tiplexer] <multiplexer name> [-enc[oding] <encoding>]

                                            [-annot[ation] <annotation>]

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

    update mul[tiplexer] -name <multiplexer name> 

                         [-enc[oding] <encoding>]

                         [-annot[ation] <annotation>]

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

    Updates a multiplexer in the currently open project.  In the first form, 

    the non-option argument is used as the name of the multiplexer to update.

    In the second, a name must be explicitly specified in option form.    

    The remainder of the options are not required but can be used to set 

    properties of the new multiplexer.

        -annotation         The annotation.

        -encoding           The MID layout type for the multiplexer, where

                                the choices are both, either, primer1, and

                                primer2.

    The four '-encoding' types have the following definitions:

        both                 Both primer 1 and primer 2 MIDs are present and

                                 necessary to determine the sample for each

                                 read.

        either               Both primer 1 and primer 2 MIDs are present, but 

                                 either one is sufficient to determine the

                                 sample.  For a given read, the MID at the

                                 5' end, in the read's orientation, is used

                                 to determine the sample.

        primer1              MIDs are only present adjacent to primer 1.

        primer2              MIDs are only present adjacent to primer 2.

    If the multiplexer was initially created without specifying the 

    '-encoding' type, the '-encoding' type must be set using the 'update 

    multiplexer' command before MIDs or MID<->Sample associations can be 

    created using the multiplexer.

    If the multiplexer already has a defined '-encoding' type and that type is

    changed, then all pre-existing sample associations for the multiplexer

    will be removed and certain pre-existing associations with MIDs may also

    be removed. Specifically, if the '-encoding' type is changed to 'either'

    and the numbers of already associated primer 1 and primer 2 MIDs are

    not equal, then both sets of MID associations will be removed.  If the

    '-encoding' type is changed to 'primer1', then any associated primer 2

    MIDs will be dissociated and if the type is changed to 'primer2', then any

    associated primer 1 MIDs will be dissociated.

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

    option.

    update proj[ect] [-annotation <annotation>]

    Updates the currently open project.  The options specify what properties of

    the project to update.

        -annotation     The annotation describing the project.

    update readData <read data name> [-annot[ation] <annotation>]

                                     [-readGroup <read group name>]

                                     [-active <boolean>]

                                     [-originalPath <original path>]

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

    update readData -name <read data name>

                    [-annot[ation] <annotation>]

                    [-readGroup <read group name>]

                    [-active <boolean>]

                    [-originalPath <original path>]

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

    Updates a read data in the currently open project.  In the first form,

    the non-option argument is used as the name of the read group to update.

    In the second, a name must be explicitly specified in option form.  The

    remainder of the options are not required but are used to set properties of

    the read data.

        -annotation     The annotation.

        -readGroup      The name of the read group to which this read data

                            belongs.

        -active         The active status of the read data.  This can be one of

                            "true" or "false".

        -originalPath   The original path of the read data.  The project

                            remembers the original path from which the read

                            data was imported.  This is used to update that

                            path.

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

    option.

    update readGroup <read group name> [-annot[ation] <annotation>]

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

    update readGroup -name <read group name>

                    [-annot[ation] <annotation>]

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

    Updates a read group in the currently open project.  In the first form, the

    non-option argument is used as the name of the read group to update.  In

    the second, a name must be explicitly specified in option form.  The

    remainder of the options are not required but are used to set properties of

    the read group.

        -annotation     The annotation.

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

    option.

    update ref[erence] <reference name> [-annot[ation] <annotation>]

                                        [-seq[uence] <sequence>]

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

    update ref[erence] -name <reference name>

                       [-annot[ation] <annotation>]

                       [-seq[uence] <sequence>]

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

    Updates a reference sequence in the currently open project.  In the

    first form, the non-option argument is used as the name of the reference

    sequence to update.  In the second, a name must be explicitly specified in

    option form.  The remainder of the options are not required but are used to

    set properties of the reference sequence.

        -annotation     The annotation.

        -sequence       The nucleotide sequence string.  This sequence must use

                            IUPAC nomenclature.

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

    option.

    update sam[ple] <sample name> [-annot[ation] <annotation>]

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

    update sam[ple] -name <sample name>

                    [-annot[ation] <annotation>]

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

    Updates a sample in the currently open project.  In the first form, the

    non-option argument is used as the name of the sample to update.  In the

    second, a name must be explicitly specified in option form.  The remainder

    of the options are not required but are used to set properties of the

    sample.

        -annotation     The annotation.

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

    option.

    update var[iant] <variant name> [-annot[ation] <annotation>]

                                    [-ref[erence] <reference sequence name>]

                                    [-pat[tern] <pattern>]

                                    [-stat[us] <status>]

                                    [-checkPat[tern] <boolean>]

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

    update var[iant] -name <new variant name>

                     [-ref[erence] <reference sequence name>]

                     [-annot[ation] <annotation>]

                     [-pat[tern] <pattern>]

                     [-stat[us] <status>]

                     [-checkPat[tern] <boolean>]

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

    Updates a variant in the currently open project.  In the first form, the

    non-option argument is used as the name of the variant to update.  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 'update variant "MyVar" -ofRef "ReferenceSequence1"' to update

    the former variant.

    The remainder of the options are not required but are used to set

    properties of the variant.

        -annotation     The annotation.

        -reference      The name of the reference sequence to which the

                            variant refers.

        -pattern        The pattern that defines the nature of this variation.

        -status         The putative status.  This can be one of "accepted",

                            "rejected", or "putative"

        -checkPattern   Whether the system should check if the variant's 

                            pattern is syntactically correct and consistent 

                            with the variant's reference sequence. The 

                            reference sequence must itself be set and have

                            a non-empty nucleotide sequence for this option

                            to take effect.  This value given must be 'true'

                            or 'false', and defaults to 'true'.

    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.