Partek Flow Documentation

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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). 


 

Numbered figure captions
SubtitleTextA new project with no samples in the Data Tab
AnchorNameA new project with no samples in the Data Tab

 

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

 

Creating a Sample Table without Data Import

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 serverMy computer, or from a URL (Figure 2).

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SubtitleTextText with attributes and filenames
AnchorNameText with attributes and filenames


The text file will be summarized as in Figure 7. Filenames that are recognized as valid file types and also located in the same folder as the text file are presented in the Files column.

 

 
Numbered figure captions
SubtitleTextSelecting the attributes, Sample ID and filenames
AnchorNameSelecting the attributes, Sample ID and filenames

 

 

Click Import and the table will be created (Figure 8). Once the table has been created, wait for a few seconds and you will notice that the server icon is animated. This means the the process of importing the files have started. Click the Queue dropdown and you can select View queued tasks... and that each file is being being imported into the project (Figure 9).

 

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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 files import tasks for each file
AnchorNameTask 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.

Once all the files have been imported from the queue, Analyses Tab will show the data node to be dark blue,

 

 
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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)

 

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 4 files were successfully imported for each sample. You can add more 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

 

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

This means the the path you will include is relative to the location of the text file. 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

 

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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"

 

Absolute path

This means the the path you will include is the full file path to the file based on the file structure of Partek Flow. Where the text file is located you can simply add the directories based on the Partek Flow home directory (see region in red box in Figure 13). 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

 

 

 

Numbered figure captions
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

 

 

Additional assistance

 

 

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Numbered figure captions
SubtitleTextText with Attributes
AnchorNameText with Attributes