Sample Table from a Text File

For new projects, a sample table can be automatically created from a tab-delimited text file. There are several advantages of creating a sample table in this manner:

You can define multiple samples and attributes even before data has been imported, allowing you to:
- customize the name of your samples, thus avoiding the automatic sample names generated based on file names
- import sample sheets as defined by the instrument that generated your data
You can simultaneously create the sample table and import data, allowing you to:
- combine several files into one sample
- import data located in multiple subdirectories

This process of generating a sample table based on a text file can only be done once per project. Additional samples or attributes can still be added using the Import data or Manage attributes buttons under the Data Tab.

Select the Text File

The text file must be created outside of Partek^® Flow^® (you can use software such as Partek^® Genomics Suite^®, Microsoft^® Excel^® or any text editor). A valid text file is a tab-delimited text file that contains one sample per row and columns containing sample information. At least one column must have unique entries and will be suggested as Sample IDs. Additional columns may contain numeric or categorical attributes and (optional) filenames. Examples of text files are shown in Figures 3 and 6.

To select the text file, create a new project and in the blank Data Tab (no samples have been imported yet), click the Assign sample attributes from a file button (Figure 1).

Figure 1. A new project with no samples in the Data Tab

Navigate to the file using the browser as shown in Figure 2. The text file may be located in either the Partek Flow server, My computer, or from a URL. However, if you wish to create the sample table and start importing the data at the same time (explained below), the text file must be on the Partek Flow server.

Check the box next to the text file that you want to use and click Next.

Figure 2. Locating a text file that contains sample information

Create the Sample Table

Text files that contain only sample IDs and attributes such as the one shown in Figure 3 can be imported to create a sample table with no associated files. For this type of import, the text file may be located in either the Partek Flow server, My computer, or from a URL (Figure 2).

Figure 3. Text with attributes

The text file will be summarized as in Figure 4. The first two columns show the headers and example terms parsed from the text file in Figure 3. The suggested attribute names can be renamed before import. Columns that contain unique entries are recognized as possible Sample IDs and can be selected using the radio button. You can choose which attributes to include and, if applicable, whether they are numeric or categorical. The Show/hide file preview link allows you to preview the text of the tab delimited text file you are using.

In the example in Figure 4, the columns for "Sample name" and "Freezer Location" are both unique and the former is selected as the Sample ID. The "Freezer location" has been deselected and it will not be included in the resulting Sample table. Since "Age" has all number terms, the Attribute type column for it is a drop down menu to choose between Numeric and Categorical. There are no filenames in the text file so the Files column is empty.

Figure 4. Selecting the attributes and Sample ID

Click Import and the table will be created (Figure 5). Click Show data files to expand the table and associate files. For more details see the Adding samples section.

Figure 5. Sample table created from a text file with attributes

Include Data Import

If you have a text file that contains sample IDs and attributes as well as the filenames of your data, you can create the sample table and start the data import at the same time. This is particularly useful for projects where multiple files are associated with the same sample (e.g., a sample ran in multiple lanes in the sequencer). For this type of import, the text file must be located in the Partek Flow server (Figure 2).

In the text file, each filename to be associated with the sample must be separated by a tab. That means, if you are using a spreadsheet software to generate the text file, there is a maximum of one file per column. You also need to add headers such as file1, file2, etc., to define the columns. There is no limit on the number of columns on the text file. It is possible to have a different number of files associated with different samples.

The filenames must show the proper extensions of data types compatible with Partek Flow (see Types of Data).

The actual files can be in the same directory as the text file or in a different directory. If the files are in a different directory, you must include the file paths (more information below).

Text file and data are in the same directory

If the text files are in the same directory as the Data files, simply include the filenames in the text file as shown in Figure 6. You do not have to specify the file path.

Figure 6. Text with attributes and filenames

Similar to the previous section, the text file will be summarized as in Figure 7. If the file types are valid, Partek Flow will recognize the filenames and locate the files within the directory. The Files column represent files to be imported.

Figure 7. Selecting the attributes, Sample ID and filenames

Click Import and the table will be created. After a few few seconds, you will notice that the server icon

will be animated (Figure 8). This means that the process of importing data files have started. Click the Queue dropdown and select View queued tasks... to see the queue of import tasks (Figure 9).

Figure 8. Sample table created from a text file and data is queued for import

Figure 9. Task Queue showing files import tasks for each file

At this stage, you can also go to the Analyses Tab of the project and see that the data node has been created but the color is light blue, which indicates the import is not complete (Figure 10, left). Once all the files have been imported from the queue, the data node will appear darker (Figure 10, right).

Figure 10. Analyses Tab showing data node during import (left) and once the import is completed (right)

To view the files associated with the data, go to the Data Tab and click Show data files to expand the table. Figure 11 shows that four files were successfully imported for each sample. You can add more or delete samples as described in the Adding samples section.

Figure 11. Expanded sample table created from a text file with attributes and associated data files

Text file and data are in different directories

If your samples are in different subdirectories, you must include the path in for your file name. You can use either a relative path or an absolute path.

Relative paths

You can use a path relative to the location of the text file you are using to create the sample table. For example in Figure 12, the text file is located in a directory called "download" while the files are in a subdirectory called MyData, then the filenames must include the path /MyData/. An example is shown below:

/MyData/NA1031_S25_L007_R1_001.fastq.gz

Figure 12. The text file is located in a directory called "download" while the files are located in a directory one level below called "MyData"

Absolute path

You can use the full path to the file based on your Partek Flow server. You must include the paths starting from the Partek Flow home directory (Figure 13, red box). For typical installations, the path begins with /home/flow/FlowData/ and so the filenames to include in the text file may look like this:

/home/flow/FlowData/download/MyData/NA1031_S25_L007_R1_001.fastq.gz

Figure 13. The Current directory (red box) shows the file path to be included in a text file containing absolute paths

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

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