Genboree

HELP TOPIC: "8.C REST API – Representations"




 
8.C.1. Introduction:

Genboree resource state is communicated via representations which are text-based formats describing the data.

By default, representations are expressed as JSON data structures. JSON is a straight-forward, cheap to generate and parse, non-verbose syntax that is excellent for communicating simple data structures. Furthermore, its syntax is similar to that of many modern programming languages and should look familiar to most developers. Also, as valid Javascript code, it is suitable for Ajax use.

Individual resources are typically expressed as JSON hashes (a.k.a. JSON objects), whose keys/properties are named fields appropriate for the specific resource.

Collections of resources are expressed as JSON arrays (lists) of individual resources.

Support for other syntaxes is also present, to some degree. YAML, for example, which has many of the aforementioned advantages, is fully supported by the API and can be used instead of JSON. XML equivalent syntax is less robust and more verbose, but is supported for resource retrieval. Finally, some resources can be or must be expressed as enhanced LFF, the native Genboree format for genome annotations and entrypoints. Requesting a non-default syntax is done via the optional format parameter.

Currently, this help document will focus on the more important issue of the resource data structures, using the default syntax (JSON).


 
8.C.2 Resource Representation Table

The table below indicates the representations for currently exposed resources. New resources will be added over time; if you wish to request a particular syntax or data structure representation for resources of interest, please contact us.

The representation types in the table encode both a data structure and the supported syntaxes. These types will be encountered in the reference links (in the refs key) to indicate the type of link, and in node names for XML.

{StructureType}_{format1}.{format2}.{format3}
e.g. 'TxtList_JSON.YAML.XML'

The representation types are clickable links to a detailed description in the next section.

 Resource: Users
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/usr/{usr}
GET
out » UsrPartial_JSON.YAML.XML or
out » UsrDetailed_JSON.YAML.XML
/REST/v1/usr/{usr}/grps
GET » [ params: detailed ]
out » TxtList_JSON.YAML.XML or
out » GrpDetailedList_JSON.YAML.XML
/REST/v1/usr/{usr}/grp/{grp}
GET
out » GrpDetailed_JSON.YAML.XML
 Resource: User Groups
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}
GET
out » GrpDetailed_JSON.YAML.XML
PUT » new name
(create or rename)
 in » GrpDetailed_JSON.YAML.XML
out » GrpDetailed_JSON.YAML.XML
/REST/v1/grp/{grp}/dbs
GET
out » TxtList_JSON.YAML.XML
/REST/v1/grp/{grp}/prjs
GET
out » TxtList_JSON.YAML.XML
PUT » new project
(name in body)
 in » Txt_JSON.YAML.XML
out » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}/usrs
GET » [ params: detailed ]
out » TxtList_JSON.YAML.XML or
out » UsrPartialList_JSON.YAML.XML
PUT » existing user(s) in group as subscriber
(name in body)
 in » TxtList_JSON.YAML.XML
out » TxtList_JSON.YAML.XML
/REST/v1/grp/{grp}/usr/{usr}
GET
out » UsrPartial_JSON.YAML.XML or
out » UsrDetailed_JSON.YAML.XML
PUT » existing user in group as subscriber
out » UsrPartial_JSON.YAML.XML or
out » UsrDetailed_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}/usr/{usr}/role
GET
out » Role_JSON.YAML.XML
PUT » existing user in group (role in body)
 in » Role_JSON.YAML.XML
out » Role_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/unlockedResources
GET
out » unlockedRefEntityList_JSON.YAML.XML
PUT » set of resources
 in » unlockedRefEntityList_JSON.YAML.XML
DELETE » set of resources
 in » unlockedRefEntityList_JSON.YAML.XML
 Resource: User Databases
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}/db/{db}
GET
out » DbDetailed_JSON.YAML.XML
PUT » new database [ params: templateName ]
 in » DbDetailed_JSON.YAML.XML
out » DbDetailed_JSON.YAML.XML
/REST/v1/grp/{grp}/db/{db}/eps
GET
out » EpDetailedList_JSON.YAML.XML or
out » EpList_LFF
PUT » new entrypoints
 in » EpDetailedList_JSON.YAML.XML or
 in » EpList_LFF
/REST/v1/grp/{grp}/db/{db}/trks
GET » [ params: detailed ]
out » TxtList_JSON.YAML.XML or
out » TrkDetailedList_JSON.YAML.XML
/REST/v1/grp/{grp}/db/{db}/seq
GET
out » FASTA
 Resource: User Projects
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}/prj/{prj}
GET
out » Txt_JSON.YAML.XML
PUT » new name;
i.e. create, rename or copy
 in » Txt_JSON.YAML.XML or
 in » Ref_JSON.YAML.XML (ref to another project for copy)
out » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/prj/{prj}/title
GET
out » Txt_JSON.YAML.XML
PUT » new title
 in » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}
/prj/{prj}/description
GET
out » Txt_JSON.YAML.XML
PUT » new description
 in » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}
/prj/{prj}/customContent
GET
out » Txt_JSON.YAML.XML
PUT » new content
 in » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}
/prj/{prj}/news
GET
out » PrjNewsList_JSON.YAML.XML
PUT » new news list
 in » PrjNewsList_JSON.YAML.XML
/REST/v1/grp/{grp}
/prj/{prj}/links
GET
out » PrjLinkList_JSON.YAML.XML
PUT » new links list
 in » PrjLinkList_JSON.YAML.XML
/REST/v1/grp/{grp}
/prj/{prj}/quickLinks
GET
out » PrjQLinkList_JSON.YAML.XML
PUT » new quick links list
 in » PrjQLinkList_JSON.YAML.XML
 Resource: Entrypoints (e.g. chromosomes)
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}
/db/{db}/ep/{ep}
GET
out » EpDetailed_JSON.YAML.XML or
out » EpList_LFF
PUT » add new entrypoints
 in » EpDetailed_JSON.YAML.XML or
 in » EpList_LFF
DELETE
 
 Resource: Annotation Tracks
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
GET » [ params: detailed ]
out » Txt_JSON.YAML.XML or
out » TrkDetailed_JSON.YAML.XML
PUT » new name;
i.e. create or rename
 in » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/url
GET
out » Txt_JSON.YAML.XML
PUT » new URL
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/urlLabel
GET
out » Txt_JSON.YAML.XML
PUT » new URL Label
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/description
GET
out » Txt_JSON.YAML.XML
PUT » new description
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/templateUrl
GET
out » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/templateUrlLabel
GET
out » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/templateDescription
GET
out » Txt_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/style
GET
out » Txt_JSON.YAML.XML
PUT » new user defined style
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/defaultStyle
GET
out » Txt_JSON.YAML.XML
PUT » new group default style
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/color
GET
out » Txt_JSON.YAML.XML
PUT » new user defined color
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/defaultColor
GET
out » Txt_JSON.YAML.XML
PUT » new group default color
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/display
GET
out » Txt_JSON.YAML.XML
PUT » new user defined display
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/defaultDisplay
GET
out » Txt_JSON.YAML.XML
PUT » new group default display
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/rank
GET
out » Txt_JSON.YAML.XML
PUT » new user defined sort order
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/defaultRank
GET
out » Txt_JSON.YAML.XML
PUT » new group default sort order
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/classes
GET
out » TxtList_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/annoAttributes
GET
out » TxtList_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/links
GET
out » TrkLinkList_JSON.YAML.XML
PUT » set of links
 in » TrkLinkList_JSON.YAML.XML or
 in » Ref_JSON.YAML.XML (containing ref to templateLinks)
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/templateLinks
GET
out » TrkLinkList_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/bigBed
GET
out » bigbed file (binary)
PUT
initiates process to create bigbed file
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/bigWig
GET
out » bigwig file (binary)
PUT
initiates process to create bigwig file
DELETE
 
 Resource: Track Attributes
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/attributes
GET
out » TxtList_JSON.YAML.XML or
out » TrkAttrDetailedList_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}/attribute/{attribute}/value
GET
out » Txt_JSON.YAML.XML
PUT » new value
 in » Txt_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}/attribute/{attribute}/display
GET
out » AttrDisplay_JSON.YAML.XML
PUT » new user defined display settings
 in » AttrDisplay_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}/attribute/{attribute}/defaultDisplay
GET
out » AttrDisplay_JSON.YAML.XML
PUT » new group default display settings
 in » AttrDisplay_JSON.YAML.XML
 Resource: Annotations
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/annos
GET » [ params: landmark, layoutName ]
 in » Layout_JSON.YAML.XML
      (only when format=layout)
out » AnnoList_LFF.LAYOUT
/REST/v1/grp/{grp}
/db/{db}/trks
/annos
GET » annos in tracks
[ params: landmark, layoutName ]
 in » TxtList_JSON.YAML.XML
      List of Track names
out » AnnoList_LFF.LAYOUT
/REST/v1/grp/{grp}
/db/{db}/trk/{trk}
/annos/count
GET » [ params: landmark ]
out » Count_JSON.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/trks
/annos/count
GET » count annos in tracks
[ params: landmark ]
 in » TxtList_JSON.YAML.XML
out » Count_JSON.YAML.XML
 Resource: Tabular Layouts
Resource Path
(rsrcPath)
Method
Type
Representation Type
(repType)
/REST/v1/grp/{grp}
/db/{db}/annos
/layout/{layout}
GET
out » Layout_JSON.YAML.XML
PUT » insert / update layout
 in » Layout_JSON.YAML.XML
DELETE
 
/REST/v1/grp/{grp}
/db/{db}/annos
/layout/{layout}
/attribute/{attribute}
GET
out » Txt_JSON.YAML.XML
PUT » change layout attribute
in » Txt.YAML.XML
/REST/v1/grp/{grp}
/db/{db}/annos
/layouts
GET
out » LayoutList_JSON.YAML.XML
PUT » insert layout
in » Layout_JSON.YAML.XML


 
8.C.3. Resource Representations

Most Genboree resources have data structure-based representations that can be formated using JSON syntax, YAML syntax, and in some cases XML syntax. A minority have specific formats that are more appropriate, such as LFF for annotations and FASTA for DNA sequence.

The current representations listed below are expressed in the default JSON syntax.

 
8.C.3.1 Common Envelope:

All data structure representations are wrapped in a simple envelope that provides status information under the status key and the data structure itself under the data key.

 Common Envelope:

{
  "data" => <jsonRepresentation>,     # One of the data strcutures below
  "status" =>
  {
    "statusCode" => "<value>",        # Status code as -text-.
    "msg" => "<value>"                # Status msg. Useful if something went wrong.
  }
}

  • - The non-data structure representations (LFF, FASTA, etc) are NOT wrapped in the common envelope.
  • - The value for the data key can null if there is an error.
  • - When sending data to the server, the status key will be ignored (it can be omitted).

 
8.C.3.2 Data Representations:

These data structures correspond to specific representations referred to in the table above. The data structure goes in place of the jsonRepresentation place-holder in the Common Envelope above.

 Count: ( repType » Count_JSON.YAML.XML )

{
  "count" : <value>                # The count (an integer)
}

 Text: ( repType » Txt_JSON.YAML.XML )

{
  "text" : "<value>",              # The text value.
  "refs" :                         # Link(s) to more info, if available, keyed by repType.
  {
    "<repType>" : "<coreURI>"
  }
}

 Text List: ( repType » TxtList_JSON.YAML.XML )

[                                  # List of Txt objects.
  {
    "text" : "<value>",            # The text value
    "refs" :                       # Link(s) to more info, if available, keyed by repType.
    {
      "<repType>" : "<coreURI>"
    }
  },
  ...
]

 Ref: ( repType » Ref_JSON.YAML.XML )

{
  "url" : <value>                # The reference URL to an API resource
}

 Unlocked Ref List: ( repType » UnlockedRefList_JSON.YAML.XML )

[                                  # List of Txt objects.	
  {
    "url" : <value>                # The reference URL to an API resource
    "key" : <value>                # The unlock key for the API resource
  },
  ...
]

 User [Detailed]: ( repType » UsrDetailed_JSON.YAML.XML )

{
  "login" : "<login>",
  "firstName" : "<firstName>",
  "lastName" : "<lastName>",
  "institution" : "<institution>",
  "telephone" : "<telephone>",
  "email" : "<email>",
  "refs" : { }
}

 User [Detailed] List: ( repType » UsrDetailedList_JSON.YAML.XML )

[
  {
    "login" : "<login>",
    "firstName" : "<firstName>",
    "lastName" : "<lastName>",
    "institution" : "<institution>",
    "telephone" : "<telephone>",
    "email" : "<email>",
    "refs" : { }
  },
  ...
]

 User [Partial]: ( repType » UsrPartial_JSON.YAML.XML )

{
  "login" : "<login>",
  "firstName" : "<firstName>",
  "lastName" : "<lastName>",
  "institution" : "<institution>",
  "email" : "<email>",
  "refs" : { }
}

 User [Partial] List: ( repType » UsrPartialList_JSON.YAML.XML )

[
  {
    "login" : "<login>",
    "firstName" : "<firstName>",
    "lastName" : "<lastName>",
    "institution" : "<institution>",
    "email" : "<email>",
    "refs" : { }
  },
  ...
]

 Group [Detailed]: ( repType » GrpDetailed_JSON.YAML.XML )

{
  "name" : "<groupName>",
  "description" : "<description>",
  "refs" : { }
}

 Group [Detailed] List: ( repType » GrpDetailedList_JSON.YAML.XML )

[
  {
    "name" : "<groupName>",
    "description" : "<description>",
    "refs" : { }
  },
  ...
]

 Role: ( repType » Role_JSON.YAML.XML )

{
  "role" : "<roleName>",               # Must be: subscriber, author or administrator
  "permissionBits" : "<value>",        # currently unimplemented
  "refs" : { }
}

 Database [Detailed]: ( repType » DbDetailed_JSON.YAML.XML )

{
  "name" : "<databaseName>",
  "refSeqId" : "<refSeqId>",           # refSeqId is a unique id. For use in composing browser URLs, etc.
  "species" : "<species>",
  "version" : "<version>",
  "description" : "<description>",
  "entrypoints" :
  {
    "count" : "<value>",               # Count of ALL the entrypoints
    "entrypoints" :                    # List of EpDetailed objects.
    [                                  # - can be a -partial- list if there are lots (>100)
      {
        "name" : "<value>",
        "length" : "<value>" ,
        "refs" :                       # Link(s) to more info, if available, keyed by repType.
        {
          "EpDetailed_JSON.YAML.XML" : "<coreURI>"   # Link to the entrypoint resource itself.
        }
      },
      ...
    ]
  },
  "refs" : { }
}

 Entrypoint/Chromosome [Detailed]: ( repType » EpDetailed_JSON.YAML.XML )

{
  "name" : "<value>",
  "length" : "<value>" ,
  "refs" : { }
}

 Entrypoint/Chromosome [Detailed] List: ( repType » DbDetailedList_JSON.YAML.XML )

{
  "count" : "<value>",                 # Count of ALL the entrypoints
  "entrypoints" :                      # List of EpDetailed objects.
  [                                    # - can be a -partial- list if there are lots (>100)
    {
      "name" : "<value>",
      "length" : "<value>" ,
      "refs" :                         # Link(s) to more info, if available, keyed by repType.
      {
        "EpDetailed_JSON.YAML.XML" : "<coreURI>"      # Link to the entrypoint resource itself.
    }
   ...
  ]
}

 Track [Detailed]: ( repType » TrkDetailed_JSON.YAML.XML )

{
  "name" : "<typeA>:<subtypeB>",
  "description" : "<value>",
  "url" : "<value>",
  "urlLabel" : "<value>",
  "annoAttributes" :                      # List of attribute names associated with track (if any)
  [                                   # . list of Txt objects
    {
      "text" : "<value>",
      "refs" : { }
    },
  ...
  ],
  "refs" : { }
}

 Track [Detailed] List: ( repType » TrkDetailedList_JSON.YAML.XML )

[
  {
    "name" : "<typeA>":"<subtypeB>",
    "description" : "<value>",
    "url" : "<value>",
    "urlLabel" : "<value>",
    "classes" :                      # List of classes (categories) associated with track (if any)
    [                                # . list of Txt objects
      {
        "text" : "<value>",
        "refs" : { }
      },
      ...
    ],
    "annoAttributes" :                   # List of attribute names associated with track (if any)
    [                                # . list of Txt objects
      {
        "text" : "<value>"
        "refs" : { }
      },
      ...
    ],
    "refs" :
    {
      "TrkDetailed_JSON.YAML.XML" : "<coreURI>"      # Link to the track resource itself.
    }
  },
  ...
]

 Track Link: ( repType » TrkLink_JSON.YAML.XML )

{
  "url" : "<value>",
  "linkText" : "<value>",
  "refs" : { }
}

 Track Link List: ( repType » TrkLinkList_JSON.YAML.XML )

[
  {
    "url" : "<value>",
    "linkText" : "<value>",
    "refs" : { }
  },
  ...
]

 Attribute Display: ( repType » AttrDisplay_JSON.YAML.XML )

{
  "color" : "<value>",
  "rank" : "<value>",
  "flags" : "<value>",
  "refs" : { }
}

 Track Attribute [Detailed]: ( repType » TrkAttrDetailed_JSON.YAML.XML )

{
  "name" : "<value>",
  "value" : "<value>",
  "display" :
  {
    "color" : "<value>",
    "rank" : "<value>",
    "flags" : "<value>",
    "refs" : { }
  }
  "defaultDisplay" :
  {
    "color" : "<value>",
    "rank" : "<value>",
    "flags" : "<value>",
    "refs" : { }
  }
  "refs" : { }
}

 Track Attribute [Detailed] List: ( repType » TrkAttrDetailedList_JSON.YAML.XML )

[
  {
    "name" : "<value>",
    "value" : "<value>",
    "display" :
    {
      "color" : "<value>",
      "rank" : "<value>",
      "flags" : "<value>",
      "refs" : { }
    }
    "defaultDisplay" :
    {
      "color" : "<value>",
      "rank" : "<value>",
      "flags" : "<value>",
      "refs" : { }
    }
    "refs" : { }
  },
  ...
]

 Project News List: ( repType » PrjNewsList_JSON.YAML.XML )

[                                   # List of ALL PrjNews items
  {                                 # . items not individually exposed (yet)
    "date" : "<date>",              # -> format: YYYY/MM/DD only (same day items sorted by texts)
    "updateText" : "<value>",       # -> could prefix with A,B,C or 1,2,3 to order same day items
    "refs" : { }
  },
  ...
]

 Project Link List: ( repType » PrjLinkList_JSON.YAML.XML )

[                                       # List of ALL PrjLink items
  {                                     # . items not individually exposed (yet)
    "url" : "<url>",
    "linkDesc" : "<value>",
    "linkText" : "<value>",
    "refs" : { }
  },
  ...
]

 Project Quick Links List: ( repType » PrjQLinkList_JSON.YAML.XML )

[                                      # List of ALL PrjQLink items
  {                                    # . items not individually exposed (yet)
    "url" : "<url>",
    "linkText" : "<value>",
    "refs" : { }
  },
  ...
]

 User [Detailed]: ( repType » UsrDetailed_JSON.YAML.XML )

{
  "login" : "<value>",
  "firstName" : "<value>",
  "lastName" : "<value>",
  "institution" : "<value>",
  "telephone" : "<value>",
  "email" : "<value>",
  "refs" : { }
}

 Tabular Layout: ( repType » Layout.YAML.XML )

{
  "name" : "<value>",              # The name of this layout.
  "description" : "<value>",       # The description of this layout.
  "userId" : "<value>",            # The ID of the user who created this layout.
  "created" : "<date>",            # The date on which this layout was created.
  "modified" : "<datetime>",       # The date / time this layout was last modified.
  "columns" : "<value>",           # A CSV list of the attributes in the order they are displayed.
                                   # The attribute names are prepended with either an 'l' or an 'a'
                                   # depending on their type.  'l' = LFF standard attribute,
                                   # 'a' = user-defined attribute.
  "sort" : "<value>",              # A CSV list of the attributes used in the sort order, encoded
                                   # the same as the "columns" field
  "groupMode" : "<value>",         # Either "terse", "verbose", or an empty string for ungrouped mode.
  "refs" :                         # Link(s) to more info, if available, keyed by repType.
  {
    "<repType>" : "<coreURI>"
  }
}

 Tabular Layout List: ( repType » LayoutList_JSON.YAML.XML )

[                                  # List of Layout objects.
  Layout,
  ...
]

 LFF Annotations List: ( repType » AnnoList_LFF.LAYOUT )

This corresponds to the [ annotations ] section in the DAS LFF format specification. See the detailed description of Genboree's enhanced LFF format for annotations, or the a user defined Tabular Layout (format=layout). Tabular Layouts are stored in the user databases or can be specified using HTTP request payloads.

 LFF Entrypoint/Chromosome List: ( repType » LffEpList )
This corresponds to the so-called [ entrypoints ] (a.k.a. [ references ]) section in the DAS LFF format specification. It is 3 tab-delimited fields: the chromosome/scaffold name, the type of entrypoing (recommendation: always use "Chromsome"), and the length in base pairs.

# EntrypointName  EntrypointType  EntrypointLength
chr1        Chromosome      247249719
chr2        Chromosome      242951149
chr20       Chromosome      62435964

 FASTA: ( repType » FASTA )
DNA sequence, in FASTA format.


 

 

 


Bioinformatics Research Laboratory
Genboree is a hosted service, but code is available free for academic use.
HGSC
© 2001-2024 Bioinformatics Research Laboratory
    (400D Jewish Wing, MS:BCM225, 1 Baylor Plaza, Houston, TX 77030, 713-798-5433)
Questions or comments?
Genboree Community Support Site