CoGeBlast Settings: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
|||
| 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: | ;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. | :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 | :'''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. | ||
| Line 28: | Line 25: | ||
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. | ;dsid: This is a [[dataset id]] for the sequence to be loaded. | ||
Latest revision as of 01:22, 10 May 2009
This page contains a detailed list of CoGeBlast settings.
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'