Partek Flow Documentation

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For new projects, a sample table can be automatically created from a tab-delimited text file.  There 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, and therefore allowing you canto:
    • Customize customize the name of your samples (and not use , thus avoiding the automatic sample names generated based on file names)
    • Import import sample sheets as defined by the instrument that generated your data
  • You can simultaneously create the sample table and import data, which allows allowing you to:
    • Combine combine several files into one sample
    • Import 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® (using other you can use software such as Partek® Genomics Suite®, Microsoft® Excel® or any other text editor). A valid text file is a tab-delimited text file that contains at one sample per row and columns containing sample information. At least one column that has must have unique entries (to and will be used suggested as Sample IDs) and may have additional columns with sample information such as experimental attributes.In a Data Tab where . 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 (Figure 1), click the Assign sample attributes values from a file button (Figure 1)
 

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new project with no samples in the Data Tab
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new project with no samples in the Data Tab

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 Navigate to the file using the browser as shown in in Figure 2. The text file may be located in either the Partek Flow serverMy computer, or from a URL.

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

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Depending on the content and location of the text file, creating the sample table can be done with or without data import. 

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SubtitleTextLocating a text file that contains sample information
AnchorNameLocating a text file that contains sample information

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Create the Sample Table

Text files that contain only sample information IDs and attributes such as the one shown in Table 1 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 serverMy computer, or from a URL (Figure 2 (If you wish to couple the table creation with data import, you must include the filenames as described in the section below on how to Include Data Import).
 

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attributes
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attributes

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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 and suggest those are recognized as possible Sample IDs.  

 

In Figure 3, the headers of the text file are presented and the user can select the Sample ID, which to be imported and 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 headers from the text file are in the first column as Attribute names, which can be edited.  Example entries are shown

 

 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

3

4, the columns for "Sample name" and "Freezer Location" are both unique and the

radio button can be used to select the preferred sample ID

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.
 


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SubtitleTextSelecting the attributes and Sample ID
AnchorNameSelecting the attributes and Sample ID

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You can also unselect the columsn you do not wish to import

 

Text can be imported as categorical attributes

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Numeric can be imported as smaple attributes

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You can rename the header.

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Click Import and the table will be created
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(Figure 5). Click Show data files to expand the table and associate files

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(see the

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Creating a Sample Table with Data Import

 

 

A feature of creating the sample ability to combine this step with data import ... the additional feature of importing samples during table creation (described below) are currently only available if the text file is in the Partek Flow Server

 

 can only be at the same time as creating the sample table) can only be performed if

 

 

 

 a sample table that also includes the locations of filenames can only be  based on the sample table (as described later in this section) 

 

 

 

The text file must be in the server or a folder that is readable by the partek flow server.  the text file contains filenames

A valid text file:

TABLE TEXT FILE NO PATH

 useful if there are many files for one sample,  You can add as many columns as you want on the right 

Flow recognizes sees that some columns in your text file are filenames of 

FIGURE OF NAVIGATION... SHOW THAT THE DATA IS IN THE SAME DIRECTORY MYDATA
FIGURE WITH FILENAMES
FIGURE RESULTING TABLE
FIGURE  IMPORT task
FIGURE  EXPANDED TABLE

 

In the example above, the text file and Data files are in the same directory. If your samples are in different subdirectories, YOU CAN USE PATHS. RELATIVE OR ABSOLUTE

Relative path

FIGURE NAVIGATION... SHOW THAT THE DATA IS DIFFERENT DIRECTORY THAN MY DATA
TABLE RELATIVE PATH

Relative to the text file

Absolute path

FIGURE NAVIGATION SHOW THAT THE DATA IS IN DIFFERENT DIRECTORY AND the directory structure starts with /home/directory....

TABLE ABSOLUTE PATH

you must write the path this way

 

For a short video of using a text file, please see. the 

 

Note that this can only be done on a blank project... once you have any import

Additional assistance

 

 

 


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SubtitleTextSample table created from a text file with attributes
AnchorNameSample table created from a text file with attributes

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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 may be located in either the Partek Flow serverMy computer, or from a URL. However, the data files should already be uploaded to the Partek Flow server (see section on file transfers). 
 
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 also 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).

Text file and data are both in server and in same directory

If the text file and the data files are both in the same directory of the Partek Flow serversimply include the filenames in the text file as shown in Figure 6. You do not have to specify the file path.
 


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SubtitleTextText with attributes and filenames
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Text file and data are in different directories

If the text file and the data files are in different directories, you must modify Figure 6 to include the file paths. For text files located in the Partek Flow serveryou can use relative or absolute file paths. For text files located in My Computer or URL you must use an absolute file path. (Remember that in either case, the data files must have already been uploaded in the Partek Flow server.) 

Relative path 

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 7, 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 would be: /MyData/NA1031_S25_L007_R1_001.fastq.gz


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SubtitleTextThe text file is located in a directory called "download" while the files are located in a directory one level below called "MyData"
AnchorNameThe text file is located in a directory called "download" while the files are located in a directory one level below called "MyData"

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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 8, 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


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SubtitleTextThe Current directory (red box) shows the file path to be included in a text file containing absolute paths
AnchorNameThe Current directory (red box) shows the file path to be included in a text file containing absolute paths

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Once you have selected the text file with filenames and/or file paths, click Next. The text file will be summarized as in Figure 9. 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.
 

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SubtitleTextSelecting the attributes, Sample ID and filenames
AnchorNameSelecting the attributes, Sample ID and filenames

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Click Import and the table will be created. After a few seconds, the server icon will be animated (Figure 10). 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 11).
 


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SubtitleTextSample table created from a text file and data is queued for import
AnchorNameSample table created from a text file and data is queued for import

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SubtitleTextTask Queue showing import tasks for each sample
AnchorNameTask Queue showing import tasks for each sample

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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 12, left). Once all the files have been imported from the queue, the data node will appear darker (Figure 12, right).
 

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SubtitleTextAnalyses Tab showing data node during import (left) and once the import is completed (right)
AnchorNameAnalyses Tab showing data node during import (left) and once the import is completed (right)

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To view the files associated with the data, go to the Data Tab and click Show data files to expand the table. Figure 13 shows that four files were successfully imported for each sample. You can add or delete samples as described in the Adding samples section.
 
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SubtitleTextExpanded sample table created from a text file with attributes and associated data files
AnchorNameExpanded sample table created from a text file with attributes and associated data files

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Additional assistance



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