|
3.4.4
|
create <entity type> <other arguments>
The 'create' command is used to create new entities. The type of entity to
create is determined by the '<entity type>' argument. The
'<other arguments>' are determined by the entity type. For example, to
create a project, you can run 'create project /path/to/new/project'. This
will create a new project at '/path/to/new/project'. To create a new
amplicon, you can run 'create amplicon "MyAmplicon"'.
The following entities are available for creation. Run
'help create <entity type>' for more detailed information.
amplicon Creates an amplicon in the currently open project.
mid Creates an MID in the currently open project.
midGroup Creates an MID group in the currently open project.
multiplexer Creates a multiplexer in the currently open project.
project Creates a new project.
readGroup Creates a read group in the currently open project.
reference Creates a reference sequence in the currently open project.
sample Creates a sample in the currently open project.
variant Creates a variant in the currently open project.
|
3.4.4.1
|
create amp[licon] <new amplicon name> [-orUpdate]
[-ofRef <reference 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>]]
create amp[licon] -name <new amplicon name>
[-orUpdate]
[-ofRef <reference 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>]]
Creates a new amplicon in the currently open project. In the first form,
the non-option argument is used as the name of the new amplicon. In the
second, a name must be explicitly specified in option form. If the
'-orUpdate' flag is given, an amplicon is only created if it does not
already exist. If it already exists, the amplicon is merely updated. The
'-ofRef' option can be used to disambiguate amplicons with the same name in
this case. The remainder of the options are not required but can be used
to set properties of the new amplicon.
-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.
|
3.4.4.2
|
create mid <new mid name> [-orUpdate]
[-seq[uence] <sequence>]
[-annot[ation] <annotation>]
[-midGroup <midGroup>]
[-checkMidGroup <boolean>]
[-file <file> [-format <format>]]
create mid -name <new mid name>
[-orUpdate]
[-seq[uence] <sequence>]
[-annot[ation] <annotation>]
[-midGroup <midGroup>]
[-checkMidGroup <boolean>]
[-file <file> [-format <format>]]
Creates a new MID in the currently open project. In the first form,
the non-option argument is used as the name of the new MID. In the
second, a name must be explicitly specified in option form. If the
'-orUpdate' flag is given, an MID is only created if it does not
already exist. If it already exists, the MID is merely updated. The
remainder of the options are not required but can be used to set
properties of the new 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,
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.
|
3.4.4.3
|
create midGroup <new midGroup name> [-orUpdate]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
create midGroup -name <new midGroup name>
[-orUpdate]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
Creates a new MID group in the currently open project. In the first form,
the non-option argument is used as the name of the new MID group. In the
second, a name must be explicitly specified in option form. If the
'-orUpdate' flag is given, an MID group is only created if it does not
already exist. If it already exists, the MID group is merely updated.
The remainder of the options are not required but can be used to set
properties of the new MID group.
-annotation The annotation.
Run 'help general tabularCommands' for information about the '-file'
option.
|
3.4.4.4
|
create mul[tiplexer] <new multiplexer name>
[-orUpdate]
[-enc[oding] <encoding>]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
create mul[tiplexer] -name <new multiplexer name>
[-orUpdate]
[-enc[oding] <encoding>]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
Creates a new multiplexer in the currently open project. In the first
form, the non-option argument is used as the name of the new multiplexer.
In the second, a name must be explicitly specified in option form. If the
'-orUpdate' flag is given, a multiplexer is only created if it does not
already exist. If it already exists, the multiplexer is merely updated.
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.
Although a multiplexer can be initially created without specifying the
'-encoding' type, the '-encoding' type must be set before MIDs and
samples can be associated with the multiplexer.
If '-orUpdate' is used to change the '-encoding' type of a multiplexer,
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', any
associated primer 1 MIDs will be dissociated.
Run 'help general tabularCommands' for information about the '-file'
option.
|
3.4.4.5
|
create proj[ect] <path for new project> [-name <new project name>]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
create proj[ect] -path <path for new project>
[-name <new project name>]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
Creates a new project. In the first form, the non-option argument is
used as the path at which the new project will be created. In the
second, a path 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 project.
When a new project is created, the previously open project is closed if
necessary, and the new project becomes the open project.
-name The name of the project.
-annotation The annotation describing the project.
Unlike with the creation of new projects from the gsAmplicon graphical user
interface (GUI), the 'create project' command does not initialize new
projects with any default contents. To initialize a project with the same
default contents as it would have if created by the GUI, the following
command should be run subsequent the 'create project' command:
utility execute %libDir/newProjectInit.ava
Run 'help general tabularCommands' for information about the '-file'
option.
Run 'help general filePaths' for more information about the interpretation
of relative paths when using the '-file' option or specifying the path for
the new project.
|
3.4.4.6
|
create readGroup <new read group name> [-orUpdate]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
create readGroup -name <new read group name>
[-orUpdate]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
Creates a new read group in the currently open project. In the first form,
the non-option argument is used as the name of the new read group. In the
second, a name must be explicitly specified in option form. If the
'-orUpdate' flag is given, a read group is only created if it does not
already exist. If it already exists, the read group is merely updated.
The remainder of the options are not required but can be used to set
properties of the new read group.
-annotation The annotation.
Run 'help general tabularCommands' for information about the '-file'
option.
|
3.4.4.7
|
create ref[erence] <new reference name> [-orUpdate]
[-annot[ation] <annotation>]
[-seq[uence] <sequence>]
[-file <file> [-format <format>]]
create ref[erence] -name <new reference name>
[-orUpdate]
[-annot[ation] <annotation>]
[-seq[uence] <sequence>]
[-file <file> [-format <format>]]
Creates a new reference sequence in the currently open project. In the
first form, the non-option argument is used as the name of the new
reference sequence. In the second, a name must be explicitly specified in
option form. If the '-orUpdate' flag is given, a reference sequence is
only created if it does not already exist. If it already exists, the
reference sequence is merely updated. The remainder of the options are not
required but can be used to set properties of the new 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.
|
3.4.4.8
|
create sam[ple] <new sample name> [-orUpdate]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
create sam[ple] -name <new sample name>
[-orUpdate]
[-annot[ation] <annotation>]
[-file <file> [-format <format>]]
Creates a new sample in the currently open project. In the first form, the
non-option argument is used as the name of the new sample. In the second,
a name must be explicitly specified in option form. If the '-orUpdate'
flag is given, a sample is only created if it does not already exist. If
it already exists, the sample is merely updated. The remainder of the
options are not required but can be used to set properties of the new
sample.
-annotation The annotation.
Run 'help general tabularCommands' for information about the '-file'
option.
|
3.4.4.9
|
create var[iant] <new variant name> [-orUpdate]
[-ofRef <reference name>]
[-annot[ation] <annotation>]
[-ref[erence] <reference name>]
[-pat[tern] <pattern>]
[-stat[us] <status>]
[-checkPat[tern] <boolean>]
[-file <file> [-format <format>]]
create var[iant] -name <new variant name>
[-orUpdate]
[-ofRef <reference name>]
[-ref[erence] <reference name>]
[-annot[ation] <annotation>]
[-pat[tern] <pattern>]
[-stat[us] <status>]
[-checkPat[tern] <boolean>]
[-file <file> [-format <format>]]
Creates a new variant in the currently open project. In the first form,
the non-option argument is used as the name of the new variant. In the
second, a name must be explicitly specified in option form. If the
'-orUpdate' flag is given, a variant is only created if it does not
already exist. If it already exists, the variant is merely updated. The
'-ofRef' option can be used to disambiguate variants with the same name in
this case. The remainder of the options are not required but can be used
to set properties of the new 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.
