Merge pull request #698 from tripal/689_tv3_ips

interproscan guide

docs/user_guide/example_genomics/func_annots/blast.rst

@@ -3,7 +3,7 @@ Adding BLAST Results
 .. note::
 
   Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../../install_tripal/drupal_home`
-  
+
 
 Adding BLAST Databases
 ----------------------
@@ -14,7 +14,7 @@ Use these values for adding the NCBI nr database:
 
 .. csv-table::
   :header: "Field Name", "Value"
-  
+
   "Name", "NCBI nr"
   "Description", "NCBI's non-redundant protein database"
   "URL", "http://www.ncbi.nlm.nih.gov/"
@@ -24,7 +24,7 @@ Use these values for adding the SwssProt database:
 
 .. csv-table::
   :header: "Field Name", "Value"
-  
+
   "Name", "ExPASy Swiss-Prot"
   "Description", "A curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases"
   "URL", "http://expasy.org/sprot/"
@@ -42,11 +42,11 @@ Within the section titled BLAST Parsing, you can specify a different, more meani
     sp|P43288|KSG1_ARATH Shaggy-related protein kinase alpha OS=Arabidopsis thaliana GN=ASK1 PE=2 SV=3
 
 
-Here the hit name is ```KSG1_ARATH```, the accession is ```P43288```, the hit description is ```Shaggy-related protein kinase alpha OS=Arabidopsis thaliana``` and the organism is ```Arabidopsis thaliana```. We need regular expressions to tell Tripal how to extract these unique parts from the match text. Because Tripal is a PHP application, the syntax for regular expressions follows the PHP method. Documentation for regular expressions used in PHP can be found here. The following regular expressions can be used to extract the hit name, the accession, hit description and organism for the example SwissProt line above:
+Here the hit name is ``KSG1_ARATH``, the accession is ``P43288``, the hit description is ``Shaggy-related protein kinase alpha OS=Arabidopsis thaliana`` and the organism is ``Arabidopsis thaliana``. We need regular expressions to tell Tripal how to extract these unique parts from the match text. Because Tripal is a PHP application, the syntax for regular expressions follows the PHP method. Documentation for regular expressions used in PHP can be found here. The following regular expressions can be used to extract the hit name, the accession, hit description and organism for the example SwissProt line above:
 
 .. csv-table::
   :header: "Element", "Regular Expression"
-  
+
   "Hit Name", ``^sp\|.*?\|(.*?)\s.*?$``
   "Hit Description", ``^sp\|.*?\|.*?\s(.*)$``
   "Hit Accession", ``^sp\|(.*?)\|.*?\s.*?$``
@@ -60,7 +60,7 @@ In the form fields, add the following values:
 
 .. csv-table::
   :header: "Field", "Value"
-  
+
   "Title for the BLAST analysis", "(leave blank)"
   "Regular expression for Hit Name", ``^sp\|.*?\|(.*?)\s.*?$``
   "Regular expression for Hit Description", ``^sp\|.*?\|.*?\s(.*)$``
@@ -89,7 +89,7 @@ Here we can save details about the analysis used to create the BLAST results.  E
 
 .. csv-table::
   :header: "Field", "Value"
-  
+
     "Name", "blastx Citrus sinensis v1.0 genes vs ExPASy SwissProt"
     "Description", "Citrus sinensis mRNA sequences were BLAST'ed against the ExPASy SwissProt protein database using a local installation of BLAST on in-house linux server. Expectation value was set at 1e-6"
     "BLAST Program", "blastx"
@@ -105,7 +105,7 @@ Create a second Analysis page for the results of the NCBI nr BLAST analysis. Use
 
 .. csv-table::
   :header: "Field", "Value"
-  
+
     "Name", "blastx Citrus sinensis v1.0 genes vs NCBI nr"
     "Description", "Citrus sinensis mRNA sequences were BLAST'ed against the NCBI non-redundant protein database using a local installation of BLAST on in-house linux server. Expectation value was set at 1e-6"
     "BLAST Program", "blastx"
@@ -120,11 +120,11 @@ First, we will load BLAST results for our citrus gene vs ExPASy SwissProt.  Now
 
 .. image:: blast4.png
 
-The top section of this page provides multiple methods for providing results file: via an upload interface, specifing a remote URL or a file path that is local to the server.  Most likely, you will always upload or provide a remote URL.  However, we download the file earlier, and stored them here: ```$DRUPAL_HOME/sites/default/files```.  So, in this case we can use the path on the local server.  Provide the following value for this form:
+The top section of this page provides multiple methods for providing results file: via an upload interface, specifying a remote URL or a file path that is local to the server.  Most likely, you will always upload or provide a remote URL.  However, we download the file earlier, and stored them here: ``$DRUPAL_HOME/sites/default/files``.  So, in this case we can use the path on the local server.  Provide the following value for this form:
 
 .. csv-table::
   :header: "Field", "Value"
-  
+
   "Server path", "sites/default/files/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out"
   "Analysis", "blastx Citrus sinensis v1.0 genes vs ExPASy SwissProt (blastall 2.2.25, Citrus sinensis mRNA vs ExPASy SwissProt)"
   "Database", "ExPASy SwissProt"
@@ -133,12 +133,12 @@ The top section of this page provides multiple methods for providing results fil
 
 .. note::
 
-  For the **Server path** we need not give the full path.  Because we downloaded the files into the Drupal directory we can leave off any preceeding path and Tripal will resolve the path.  Otherwise we could provide the full path.
-  
+  For the **Server path** we need not give the full path.  Because we downloaded the files into the Drupal directory we can leave off any preceding path and Tripal will resolve the path.  Otherwise we could provide the full path.
+
 .. note::
 
   Specifying **ExPASy SwissProt** as the database will allow the importer to use the database configuration settings we entered earlier.
-  
+
 Clicking the **Import BLAST file** will add a job which we can manually execute with the following command:
 
 ::
@@ -149,7 +149,7 @@ The results should now be loaded. Now we want to add the results for NCBI nr. Re
 
 .. csv-table::
   :header: "Field", "Value"
-  
+
   "Server path", "sites/default/files/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_nr.out"
   "Analysis", "blastx Citrus sinensis v1.0 genes vs ExPASy SwissProt (blastall 2.2.25, Citrus sinensis mRNA vs NCBI nr)"
   "Database", "ExPASy SwissProt"
@@ -166,7 +166,7 @@ To view results we must find the mRNA that has BLAST hits.  For this example, cl
 
 .. image:: blast5.png
 
-Notice, that when viewing the results, the SwissProt maches are links.  When clicked they redirect the user to the SwissProt website where users can find more information about that protein.
+Notice, that when viewing the results, the SwissProt matches are links.  When clicked they redirect the user to the SwissProt website where users can find more information about that protein.
 
 .. image:: blast6.png
 

docs/user_guide/example_genomics/func_annots/interpro.rst

@@ -1,2 +1,80 @@
 Adding InterProScan Results
-===========================
+===========================
+
+.. note::
+
+  Remember you must set the ``$DRUPAL_HOME`` environment variable if you want to cut-and-paste the commands below. See :doc:`../../install_tripal/drupal_home`
+
+For this tutorial, these results were obtained by using a local installation of InterProScan installed on a computational cluster. However, you may choose to use Blast2GO or the online InterProScan utility. Results should be saved in ``XML`` format.
+
+
+What is InterProScan?
+---------------------
+To learn more about InterProScan, please visit https://www.ebi.ac.uk/interpro/
+
+
+Create the Analysis Page
+-------------------------
+
+  .. note::
+
+    It is always recommended to create an analysis page anytime you import data. The purpose of the analysis page is to describe how the data being added was derived or collected.
+
+Tripal defines the **InterPro Results** Bundle, which is a specific type of Chado analysis.  Create a new record by going to ``Content -> Tripal Content -> Add Tripal Content --> InterPro Results``.
+
+Fill out the fields as described in the table below.
+
+
+.. csv-table::
+  :header: "Field", "Value"
+
+  "Name", "InterPro Annotations of C. sinensis v1.0"
+  "InterPro Program", "InterProScan"
+  "InterPro Version", "4.8"
+  "Date Performed", "Current Date"
+  "Data Source Name", "C. sinensis v1.0 mRNA"
+  "Data Source Version", "v1.0"
+  "Data Source URI", "n/a"
+  "Description", "Materials & Methods: C. sinensis mRNA sequences were mapped to IPR domains and GO terms using a local installation of InterProScan executed on a computational cluster. InterProScan date files used were MATCH_DATA_v32, DATA_v32.0 and PTHR_DATA v31.0."
+
+Press the **Save** button.
+
+Import the InterProScan XML results
+------------------------------------
+
+
+Next, we will load InterProScan results for our citrus gene.  To do this, navigate to **Tripal > Data Loaders > Chado InterProScan XML results loader**.  The following page will be presented:
+
+.. image:: interpro1.png
+
+The top section of this page provides multiple methods for providing results file: via an upload interface, specifying a remote URL or a file path that is local to the server.  Most likely, you will always upload or provide a remote URL.  However, we downloaded the files earlier, and stored them here: ``$DRUPAL_HOME/sites/default/files``.  So, in this case we can use the path on the local server.  Provide the following value for this form:
+
+.. csv-table::
+  :header: "Field", "Value"
+
+  "Server path", "sites/default/files/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml"
+  "Analysis", "InterPro Annotations of C. sinensis v1.0"
+  'Load GO terms to the database', 'unchecked'
+  "Query Name RE", ""
+  "Use Unique Name", "unchecked"
+  "Query Type", "mRNA"
+
+In order for GO terms to be imported, the Gene Ontology must be loaded on your site: for this tutorial, we leave the box unchecked.
+
+
+.. note::
+
+  For the **Server path** we need not give the full path.  Because we downloaded the files into the Drupal directory we can leave off any preceding path and Tripal will resolve the path.  Otherwise we could provide the full path.
+
+
+
+Clicking the **Import InterProScan file** will add a job which we can manually execute with the following command:
+
+::
+
+    drush trp-run-jobs --username=administrator --root=$DRUPAL_HOME
+
+
+After the job is run, our InterPro field will be populated on the mRNA page with an annotation diagram:
+
+.. image:: interpro2.png