Importing sequence

It is possible to import sequence that has been stored in a text file. Such a file may be created manually or generated automatically by an external application or script, for example by a LIMS. Importing a sequence in this way allows Clarity to prepare the measurement workflow based on data received from other systems.

Clarity supports several file formats for this purpose, including *.txt, *.csv and *.prn. Values have to be in delimited format and separated by an arbitrary delimiter.

To create a sequence table from an imported file follow the steps below:

  1. Open the Sequence window and select File - Import… ①. This opens the Import Sequence Step 1 dialog, which opens in the directory defined in chapter "Setting up custom export and import directories".

  2. Select the file to be imported ⓐ.
  3. Select the character used as delimiter ⓑ (possible options are <TAB>, <SPACE>, <COMMA> or <SEMICOLON>) and decimal delimiter ⓒ (possible options are <Windows Locale>, <COMMA>, <DOT> or <SEMICOLON>).
  4. If the text file to be imported contains column headers in the first row, use First Row Is Header ⓓ checkbox. This row is used for matching in the Import Sequence Step 2 dialog.
  5. Preview of the first five rows of the imported sequence table is displayed in the bottom part of the dialog ⓔ.
  6. Click Next to continue ⓕ.

  7. Set the Column Matching ⓖ to match the imported columns with the ones present in Clarity Sequence table. Start vial number and File Name are required columns and are therefore shown in bold.

If the imported file contains column headers (the First Row is Header option was selected in Step 1), Clarity will try to match the columns automatically based on their names. Any manual changes will overwrite this automatic matching. Clarity will remember the final matching for future imports.

  1. Select whether you want to save imported sequence as a new file or just append it to currently opened one ⓗ.
  2. You can also use three additional checkboxes ⓘ to adjust the import behaviour:
    • Save Sequence and Delete Import File - invokes Save as dialog to save the imported sequence and deletes the imported file.
    • Save Import Settings - stores current settings so they will be used automatically for future imports.
    • Show Sequence Options – opens the Sequence Options dialog immediately after the import finishes, allowing you to adjust additional parameters before the sequence is created.
  3. Press the Finish button to complete the import and close the dialog ⓙ.

Clarity also provides command-line parameters that can be used to automate the import process (full list of all available command-line parameters together with their detailed description can be found in Reference Guide):

seq_import

Imports the specified *.txt file as a sequence and replaces the currently opened sequence. The command is ignored when a sequence is already running. The imported sequence is loaded under the default name Noname, therefore the seq_save_as command must be used to save it before starting a run.

  • Example: Clarity.exe i=1 seq_import="C:\CLARITY\DataFiles\<PROJECT>\seq.txt"

seq_save_as

Saves the active sequence under the specified name. The command is ignored when the sequence is running.

  • Example: Clarity.exe i=1 seq_save_as="C:\CLARITY\DataFiles\<PROJECT>\results.seq"

seq_import_append

Imports the specified file and appends its content to the currently open sequence. It uses the same settings as when the import is performed manually.

  • Example: Clarity.exe i=1 seq_import_append="C:\CLARITY\DataFiles\<PROJECT>\seq.txt"