A script must start with a newProject or openProject command.

newProject

Same as the File > New menu command. Creates a new, untitled project.

(none)

openProject

Same as the File > Open menu command. Opens an existing project.

file (required)

Specifies the filename and directory of the project you wish to open. The pathname\filename you wish to open must exist, must have the extension “.sqd,” and must be enclosed in quotes.

openProject

file:"pathname\filename.sqd"

importProject

Same as the File > Import menu command. Imports an existing Sequencher 4.2 or Phrap project.

file (required)

Specifies the filename and directory of the project to be imported. The pathname\filename must exist and must be enclosed in quotes. If desired, you may leave off a specific file name and import all valid files within a folder.

This example will convert all Phrap or Sequencher 4.2 projects located in the C:\assembly directory to SeqMan projects and save them in the C:\ExportFolder directory:

importProject

file:"C:\assembly"

destination:"C:\ExportFolder"

destination (optional)

Specifies the name and or folder for the SeqMan project being created from the imported file. The pathname\filename must exist and must be enclosed in quotes.

loadReference

Adds a reference sequence to a project for Variant Discovery.

file (required)

Specifies the directory and file name of the sequence file(s) to be loaded. A folder may also be specified, in which case all of the sequence files within that folder will be loaded. The directory and file/folder name must be enclosed in quotes. If a folder is specified, a final backslash “\” is necessary.

loadSeq

Adds sequences to a project.

file (required)

Specifies the directory and file name of the sequence file(s) to be loaded. A folder may also be specified, in which case all of the sequence files within that folder will be loaded. The directory and file/folder name must be enclosed in quotes. If a folder is specified, a final backslash “\” is necessary.

loadSeq

file:"pathname\folder\"

contaminantFile:"pathname\filename.seq"

contaminantFile (optional)

Specifies the directory and file name of the contaminant sequence file to be used for contaminant scanning. A folder may also be specified, in which case all of the sequence files within that folder will be loaded. The directory and file/folder name must be enclosed in quotes. To use contaminant scanning, the contamScan parameter for the assemble command must be set to true.

setDefaultDirectory (optional)

Defines the default directory for the project. When a default directory is specified, files located in that directory only need to be identified by their subfolder and/or file name in subsequent commands.

defaultWinDirectory

or

defaultMacDirectory (one is required)

Specifies the directory to be used as the default on a Windows/Macintosh computer. The directory must exist and must be enclosed in quotes.

On Windows:

setDefaultDirectory

defaultWinDirectory:"C:\ABC_proj\"

On Macintosh:

setDefaultDirectory

defaultMacDirectory:"/Library/ABC_proj/"