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how_to:exportpride [2011/03/08 14:50] 132.168.74.230 |
how_to:exportpride [2013/01/28 08:05] (current) 132.168.72.131 |
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**Warning:** | **Warning:** | ||
* :!: **Exporting a UserContext to PRIDE XML format is only available for [[http://biodev.extra.cea.fr/docs/irma/doku.php?id=msidb|MSIdb]] version D.4 (or later versions).** | * :!: **Exporting a UserContext to PRIDE XML format is only available for [[http://biodev.extra.cea.fr/docs/irma/doku.php?id=msidb|MSIdb]] version D.4 (or later versions).** | ||
- | * :!: **In the current hEIDI version (v1.10.1 / MSIdb E.1), the ''header'' of the generated PRIDE XML file is not totally achieved** (contact info, experiment & sample details, protocol steps, etc.). **The user will have to use PRIDE Converter to build another PRIDE XML file, from which he will only copy the meta-infos and paste them into the hEIDI generated PRIDE XML file.** | + | * :!: **In hEIDI versions v1.10.1, v1.11.0 and up to now (MSIdb E.1), the ''header'' of the generated PRIDE XML file is not totally achieved** (contact info, experiment & sample details, protocol steps, etc.). **The user will have to use PRIDE Converter to build another PRIDE XML file, from which he will only copy the meta-infos and paste them into the hEIDI generated PRIDE XML file.** |
**Note:** | **Note:** | ||
- | * Only typical proteins of each protein group will be exported | + | * Only visible typical proteins of each protein group will be exported |
===== Main steps to export a UserContext to PRIDE XML format ===== | ===== Main steps to export a UserContext to PRIDE XML format ===== | ||
- **From a UserContext in hEIDI**, launch the PRIDE XML Export to create a first PRIDE XML file (see details below) | - **From a UserContext in hEIDI**, launch the PRIDE XML Export to create a first PRIDE XML file (see details below) | ||
+ | - If necessary, a dialog will appear (see below), [[how_to:spectrummatchfeeder|import spectra into MSIdb]]. | ||
- **From the PRIDE Converter wizard**, create a second PRIDE XML file (see **[[userguide:pride_converter|here]]**) | - **From the PRIDE Converter wizard**, create a second PRIDE XML file (see **[[userguide:pride_converter|here]]**) | ||
- **Copy the ''header'' from the second PRIDE XML file and paste it into the first PRIDE XML file** (see below) | - **Copy the ''header'' from the second PRIDE XML file and paste it into the first PRIDE XML file** (see below) | ||
- Check your modified PRIDE XML file using **[[userguide:pride_inspector|PRIDE Inspector]]** | - Check your modified PRIDE XML file using **[[userguide:pride_inspector|PRIDE Inspector]]** | ||
- | |||
===== 1. Launch PRIDE XML Export from hEIDI ===== | ===== 1. Launch PRIDE XML Export from hEIDI ===== | ||
- | Follow these steps to generate a PRIDE XML file from a given context: {{ :how_to:prideexport_compo_1.png|}} | + | Follow these steps to generate a PRIDE XML file from a given context: {{ :how_to:prideexport_compo_1_new.png|}} |
* **After having [[how_to:createproject|created ]]or [[how_to:loadproject|opened an hEIDI project]], [[how_to:opensession|open your MSI session]]** but :!: **Don't forget to __activate__ your hEIDI project**. | * **After having [[how_to:createproject|created ]]or [[how_to:loadproject|opened an hEIDI project]], [[how_to:opensession|open your MSI session]]** but :!: **Don't forget to __activate__ your hEIDI project**. | ||
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* **Select ''MS Identifications > Context > Export > PRIDE XML''** | * **Select ''MS Identifications > Context > Export > PRIDE XML''** | ||
* **Enter a name for your PRIDE XML file and browse to the directory of your choice** (default is to use the name of the selected UserContext with the .xml extension in the hEIDI project directory). | * **Enter a name for your PRIDE XML file and browse to the directory of your choice** (default is to use the name of the selected UserContext with the .xml extension in the hEIDI project directory). | ||
- | * **[Optional]** A dialog may appear if spectra are missing | + | * **[WARNING]** A dialog may appear if spectra are missing |
- | * Answer ''No'' if you want to stop the PRIDE XML Export process (you will then need to populate the MSIdb using the SpectrumMatchFeeder tool) | + | * Answer ''No'' to stop the PRIDE XML Export process (Ask the INFO Team to populate the MSIdb with missing spectra) |
- | * Answer ''Yes'' if you want hEIDI to launch for you the tool to populate MSIdb with missing spectra | + | |
- | * **Check the Mascot data root path**. You can keep the default value (''\\cp-mascot\data'') or use the corresponding Drive Letter you have set up in Windows Explorer, for example ''Y:''. Check, in Windows Explorer, you have mapped a drive to the Mascot data folder (\\cp-mascot\data) and you are connected to that folder. | + | |
- | * **Click ''Ok, populate MSIdb with missing info''** to update database | + | |
- | * A dialog will appear when MSIdb is populated with missing spectra and **ask you to relaunch PRIDE XML Export**. | + | |
* If PRIDE XML Export ended successfully, **a dialog message is displayed at the end of the export process** {{ :how_to:prideexport_success.png |}} | * If PRIDE XML Export ended successfully, **a dialog message is displayed at the end of the export process** {{ :how_to:prideexport_success.png |}} | ||
+ | * A dialog appears to display the log file (see [[how_to:exportpridelog|]] for more details) | ||
- | :!: **Open the resulting .xml Pride file out of hEIDI using any external text editor**. Opening the file in the hEIDI environment may cause memory issue if the file size is too big | + | * :!: **Open the resulting .xml Pride file out of hEIDI using any external text editor**. Opening the file in the hEIDI environment may cause memory issue if the file size is too big |
==== The ''runDescriptor.properties'' file ==== | ==== The ''runDescriptor.properties'' file ==== | ||
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===== 4. Check your PRIDE XML file using PRIDE Inspector ===== | ===== 4. Check your PRIDE XML file using PRIDE Inspector ===== | ||
- |