Difference between revisions of "WS224 Models.wrm"

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[[WormBase_Models#Model_Change_Summaries |Back]]
 
[[WormBase_Models#Model_Change_Summaries |Back]]
  
 +
__TOC__
 
== Models Tagged for WS224 ==
 
== Models Tagged for WS224 ==
  
−
<pre>This cycle there were 2 proposed model changes to the ?Strain Class and some acedb magic tags added/moved.
+
This cycle there were 2 proposed model changes to the ?Strain Class and the reorganisation of some of the tags in the method model.
 +
 +
This will effect groups that have an old version of the methods loaded into their databases.
 +
 +
1/2) ?Strain Class
 +
 +
Addition of inbreeding states Selfed, Isofemale, Multifemale and Inbred.
 +
 +
Addition of more landscapes, Botanical_garden_zoo, Wet_shrubland and Dry_shrubland.
 +
Change for Wild_forest -> Forest.
 +
 +
3) ?Method
 +
Addition of the top level tag Align_mapping and downstream tags.
 +
These additions/changes were take from the core ACeDB models.wrm as these are used by more modern binaries.
 +
 +
Our Method model remains backwards compatible but it is worth re-reading the current misc_autoace_models file available from Sanger
 +
 +
[http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/autoace_config/misc_autoace_methods.ace?root=ensembl&view=log misc_autoace_methods.ace]
 +
 +
== Model Changes ==
  
−
1) ?Strain Class
+
Human readable diff:
−
 
+
−
?Strain  Properties Males Text
+
?Strain
−
                    Inbreeding_state UNIQUE Selfed Text
+
  -------
−
                                            Isofemale Text
+
   
−
                                            Multifemale Text
+
>     Inbreeding_state UNIQUE Selfed Text
−
                                            Inbred Text  
+
>                                            Isofemale Text
−
 
+
>                                            Multifemale Text
−
         Isolation Landscape UNIQUE Urban_garden
+
>                                            Inbred Text
−
                                    Forest
+
−
                                    Wild_grassland
+
<     Wild_forest
−
                                    Agricultural_land
+
---
−
                                    Oasis
+
>     Forest
−
                                    Rural_garden
+
−
                                    Botanical_garden_zoo
+
>     Botanical_garden_zoo
−
                                    Wet_shrubland
+
>                                  Wet_shrubland
−
                                    Dry_shrubland
+
>                                  Dry_shrubland 
 +
 +
 +
?Method
 +
-------
 +
 +
Descriptions and text:
 +
 +
< Display No_display
 +
---
 +
> Display No_display // column is not displayed at all.
 +
 +
< CDS_colour #Colour
 +
---
 +
> CDS_colour #Colour // CDS outlined in this colour.
 +
 +
< Percent // '%' in text, + default bounds 25, 100
 +
---
 +
> Percent // Score will be displayed as a '%' in fmap reportline + bounds default to 25 & 100.
 +
 +
< Symbol UNIQUE Text // first char only is used
 +
---
 +
> Symbol UNIQUE Text         // first char only is used
 +
 +
< Max_mag UNIQUE Float // don't show if more bases per line
 +
< Min_mag UNIQUE Float // don't show if fewer bases per line
 +
< Show_text      // only put text in right-hand column if set
 +
< Join_blocks // link up all blocks of a single feature with lines
 +
---
 +
> Max_mag UNIQUE Float        // don't show if more bases per line
 +
> Min_mag UNIQUE Float        // don't show if fewer bases per line
 +
> Show_text                  // only put text in right-hand column if set
 +
> Join_blocks                // link up all blocks of a single feature with lines
 +
> Display_gaps                // draw sequences or homols with gaps
 +
 +
 +
> EMBL_dump EMBL_feature UNIQUE Text // require this
 +
>   EMBL_threshold UNIQUE Float // apply to score unless overridden
 +
>   EMBL_qualifier Text UNIQUE Text
 +
>   // if 1 Text, it is the entire qualifier including '/'
 +
>   // if 2 Texts, 1st is an sprintf format and 2nd is
 +
>   //  an argument.  If this is "score", "note", "y1", "y2" or "target"
 +
>   //  then use the corresponding field of the Feature or Homol line.
 +
>   // multiple formats will be concatenated until one starts with '/'.
 +
> EMBL_dump_info #EMBL_dump_info // when used for controlling dump 
 +
---
 +
< EMBL_dump_info #EMBL_dump_info
 +
< EMBL_dump EMBL_feature UNIQUE Text // require this
 +
<   EMBL_threshold UNIQUE Float // apply to score unless overridden
 +
<   EMBL_qualifier Text UNIQUE Text
 +
<   // if 1 Text, it is the entire qualifier including '/'
 +
<   // if 2 Texts, 1st is an sprintf format and 2nd is
 +
<   //  an argument.  If this is "score", "note", "y1", "y2" or "target"
 +
<   //  then use the corresponding field of the Feature or Homol line.
 +
<   // multiple formats will be concatenated until one starts with '/'.
 +
 +
< GFF_feature UNIQUE ?SO_term
 +
---
 +
> GFF_feature UNIQUE Text
 +
 +
 +
Alignment Method update:
 +
<              Gapped // draw sequences or homols with gaps
 +
<              Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override.
 +
---
 +
>              Display_gaps                // draw sequences or homols with gaps
 +
>              Gapped                      // draw sequences or homols with gaps //leaving this is preserved backwards compatibility
 +
>        // Alignment options (default is map only with no misaligns or clipping and do not map gaps).
 +
>        Align_mapping Allow_misalign        // Homol reference/match coords do not have to align exactly, ref coords override.
 +
>                      Allow_clipping        // Map gaps even if they need to be clipped.
 +
>                      Map_gaps              // Map gaps for gapped aligns.

Latest revision as of 13:55, 13 January 2011

Back

Models Tagged for WS224

This cycle there were 2 proposed model changes to the ?Strain Class and the reorganisation of some of the tags in the method model.

This will effect groups that have an old version of the methods loaded into their databases.

1/2) ?Strain Class

Addition of inbreeding states Selfed, Isofemale, Multifemale and Inbred. 

Addition of more landscapes, Botanical_garden_zoo, Wet_shrubland and Dry_shrubland.
Change for Wild_forest -> Forest.

3) ?Method
Addition of the top level tag Align_mapping and downstream tags.
These additions/changes were take from the core ACeDB models.wrm as these are used by more modern binaries.

Our Method model remains backwards compatible but it is worth re-reading the current misc_autoace_models file available from Sanger

misc_autoace_methods.ace

Model Changes

Human readable diff:

?Strain
-------

> 		     Inbreeding_state UNIQUE Selfed Text
>                                            Isofemale Text
>                                            Multifemale Text
>                                            Inbred Text  

< 				    Wild_forest
---
> 				    Forest 

> 				    Botanical_garden_zoo
>                                   Wet_shrubland
>                                   Dry_shrubland  


?Method
-------

Descriptions and text:

< 	Display No_display
---
> 	Display No_display			// column is not displayed at all. 

< 		CDS_colour #Colour
---
> 		CDS_colour #Colour		// CDS outlined in this colour.

< 			Percent // '%' in text, + default bounds 25, 100
---
> 			Percent // Score will be displayed as a '%' in fmap reportline + bounds default to 25 & 100.

< 		Symbol UNIQUE Text	// first char only is used
---
> 		Symbol UNIQUE Text          // first char only is used

< 		Max_mag UNIQUE Float	// don't show if more bases per line
< 		Min_mag UNIQUE Float	// don't show if fewer bases per line
< 		Show_text      // only put text in right-hand column if set
< 		Join_blocks // link up all blocks of a single feature with lines
---
> 		Max_mag UNIQUE Float        // don't show if more bases per line
> 		Min_mag UNIQUE Float        // don't show if fewer bases per line
> 		Show_text                   // only put text in right-hand column if set
> 		Join_blocks                 // link up all blocks of a single feature with lines
> 		Display_gaps                // draw sequences or homols with gaps 


> 	EMBL_dump EMBL_feature UNIQUE Text		// require this
> 		  EMBL_threshold UNIQUE Float		// apply to score unless overridden
> 		  EMBL_qualifier Text UNIQUE Text
> 	  // if 1 Text, it is the entire qualifier including '/'
> 	  // if 2 Texts, 1st is an sprintf format and 2nd is
> 	  //   an argument.  If this is "score", "note", "y1", "y2" or "target"
> 	  //   then use the corresponding field of the Feature or Homol line.
> 	  // multiple formats will be concatenated until one starts with '/'.
> 	EMBL_dump_info #EMBL_dump_info // when used for controlling dump  
---
< 	EMBL_dump_info #EMBL_dump_info
< 	EMBL_dump EMBL_feature UNIQUE Text		// require this
< 		  EMBL_threshold UNIQUE Float		// apply to score unless overridden
< 		  EMBL_qualifier Text UNIQUE Text
< 	  // if 1 Text, it is the entire qualifier including '/'
< 	  // if 2 Texts, 1st is an sprintf format and 2nd is
< 	  //   an argument.  If this is "score", "note", "y1", "y2" or "target"
< 	  //   then use the corresponding field of the Feature or Homol line.
< 	  // multiple formats will be concatenated until one starts with '/'.

< 		GFF_feature UNIQUE ?SO_term
---
> 		GFF_feature UNIQUE Text


Alignment Method update:
<               Gapped // draw sequences or homols with gaps
<               Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override. 
---
>               Display_gaps                // draw sequences or homols with gaps 
>               Gapped                      // draw sequences or homols with gaps //leaving this is preserved backwards compatibility
>         // Alignment options (default is map only with no misaligns or clipping and do not map gaps).
>         Align_mapping Allow_misalign        // Homol reference/match coords do not have to align exactly, ref coords override.
>                       Allow_clipping        // Map gaps even if they need to be clipped.
>                       Map_gaps              // Map gaps for gapped aligns.
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