To create a script, type a list of commands in the SeqMan Pro scripting language using a text editor, and then save the list as a text file with a .script extension. (e.g., filename.script). The following table shows rules and examples for writing a script:
|
Rule |
Example |
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Scripting commands for SeqMan should be written in the format shown at right. |
commandname parameter:value |
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Commands that have multiple parameters should be written with all of the parameters on one line, each separated by a space. |
Commandname parameter1:value parameter2:value parameter3:value |
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The one exception to this rule is the setParam command, which can be repeated on a new line for each parameter. |
setParam matchSize:25 setParam minMatchPercent:80 setParam gapPenalty:0.25 |
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Parameters that have more than one value should be written with the group of values enclosed in { } brackets, and each value separated by a space. |
Commandname parameter:{value1 value2 value3 value4} |
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To add a comment to a script, precede the comment with a semi-colon. |
;sample comment |
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To prevent a command from being executed without deleting it from the script, type a semi-colon immediately before the command. |
;commandname parameter:value |
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All parameters that require a file name or directory value must have the file name/directory enclosed in quotes. |
saveProject file: "C:\SMPro\abc_project.sqd" |
Many parameters have default values that are used when no parameter is specified. If you want to use the default value for a parameter, it is not necessary to write that parameter in your script.
To execute the finished script, highlight the name of the script file from where you saved it (use Windows Explorer or Finder on Macintosh), and then drag and drop the file onto the SeqMan application window.