Difference between revisions of "CoGeBlast Settings"
From CoGepedia
(Created page with 'This page contains a detailed list of CoGeBlast settings. == URL Parameters == The general URL parameters for CoGeBlast are as follows: <blockquote><nowiki>CoGeBlast.pl?pa...') |
(→URL Parameters) |
||
| (2 intermediate revisions by one other user not shown) | |||
| Line 4: | Line 4: | ||
The general URL parameters for CoGeBlast are as follows: | The general URL parameters for CoGeBlast are as follows: | ||
| − | + | <pre><nowiki>CoGeBlast.pl?param_name1=<parameter>¶m2=<parameter>¶m3=<parameter> etc. </nowiki></pre> | |
| − | < | + | |
| − | + | ||
URL parameters are used to load sequences into CoGeBlast. There are two methods of doing this: using [[Feature]]s, or using [[Dataset]]s | URL parameters are used to load sequences into CoGeBlast. There are two methods of doing this: using [[Feature]]s, or using [[Dataset]]s | ||
=== Parameters Utilizing Features === | === Parameters Utilizing Features === | ||
| − | |||
General form: | General form: | ||
| + | <pre>CoGeBlast.pl?fid=1234&fid=5678&fid=...&rc=0&gstid=3</pre> | ||
| − | + | ;fid:This is a list of [[feature id]]s that instruct CoGeBlast to load sequences associated with the features the feature ids represent. An example is below: | |
| − | + | :<pre>CoGeBlast.pl?fid=1234&fid=5678</pre> | |
| − | + | :The above ... indicates that any number of fids may be strung together in the URL. | |
| + | :'''Note:''' No numbering is associated with the "fid" - i.e the parameter list | ||
| − | < | + | :<pre>CoGeBlast.pl?fid1=1234&fid2=5678</pre> |
| − | + | :is '''incorrect''' and will result in sequences not being properly loaded. | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | is '''incorrect''' and will result in sequences not being properly loaded. | + | |
=== Parameters Utilizing Datasets === | === Parameters Utilizing Datasets === | ||
| − | |||
General form: | General form: | ||
| − | < | + | <pre> CoGeBlast.pl?dsid=51223&chr=3&upstream=4562&downstream=9042&rc=0&gstid=3 </pre> |
| − | + | ;dsid: This is a [[dataset id]] for the sequence to be loaded. | |
| − | + | ;chr: This is the [[chromosome]] from the dataset associated with the dataset id. | |
| − | This is a [[dataset id]] for the sequence to be loaded. | + | ;upstream: This represents the start position of the sequence on the chromosome selected. |
| − | + | ;downstream: This represents the stop position of the sequence on the chromosome selected. | |
| − | + | ||
| − | + | ||
| − | This is the [[chromosome]] from the dataset associated with the dataset id. | + | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | This represents the start position of the sequence on the chromosome selected. | + | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | This represents the stop position of the sequence on the chromosome selected. | + | |
=== Parameters Utilized In General === | === Parameters Utilized In General === | ||
| − | + | ;rc: Select whether or not to reverse complement the sequence(s) being entered into CoGeBlast. Boolean value, with 0 being no reverse complementation, and 1 being yes. | |
| − | + | ;gstid: ''''TODO'''' | |
| − | + | ||
| − | Select whether or not to reverse complement the sequence(s) being entered into CoGeBlast. Boolean value, with 0 being no reverse complementation, and 1 being yes. | + | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | ''''TODO'''' | + | |
Latest revision as of 19:22, 9 May 2009
This page contains a detailed list of CoGeBlast settings.
Contents
URL Parameters
The general URL parameters for CoGeBlast are as follows:
CoGeBlast.pl?param_name1=<parameter>¶m2=<parameter>¶m3=<parameter> etc.
URL parameters are used to load sequences into CoGeBlast. There are two methods of doing this: using Features, or using Datasets
Parameters Utilizing Features
General form:
CoGeBlast.pl?fid=1234&fid=5678&fid=...&rc=0&gstid=3
- fid
- This is a list of feature ids that instruct CoGeBlast to load sequences associated with the features the feature ids represent. An example is below:
CoGeBlast.pl?fid=1234&fid=5678
- The above ... indicates that any number of fids may be strung together in the URL.
- Note: No numbering is associated with the "fid" - i.e the parameter list
CoGeBlast.pl?fid1=1234&fid2=5678
- is incorrect and will result in sequences not being properly loaded.
Parameters Utilizing Datasets
General form:
CoGeBlast.pl?dsid=51223&chr=3&upstream=4562&downstream=9042&rc=0&gstid=3
- dsid
- This is a dataset id for the sequence to be loaded.
- chr
- This is the chromosome from the dataset associated with the dataset id.
- upstream
- This represents the start position of the sequence on the chromosome selected.
- downstream
- This represents the stop position of the sequence on the chromosome selected.
Parameters Utilized In General
- rc
- Select whether or not to reverse complement the sequence(s) being entered into CoGeBlast. Boolean value, with 0 being no reverse complementation, and 1 being yes.
- gstid
- 'TODO'
