CoGeBlast Settings: Difference between revisions
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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...' |
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<blockquote> CoGeBlast.pl?fid=1234&fid=5678&fid=...&rc=0&gstid=3 </blockquote> | <blockquote> CoGeBlast.pl?fid=1234&fid=5678&fid=...&rc=0&gstid=3 </blockquote> | ||
* fid | *; 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: | |||
:<blockquote>CoGeBlast.pl?fid=1234&fid=5678</blockquote> | |||
: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 | |||
''' | :<blockquote>CoGeBlast.pl?fid'''1'''=1234&fid'''2'''=5678</blockquote> | ||
: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 === | ||
| Line 33: | Line 32: | ||
General form: | General form: | ||
<blockquote> CoGeBlast.pl?chr=3&upstream=4562&downstream=9042&rc=0&gstid=3 </blockquote> | <blockquote> CoGeBlast.pl?dsid=51223&chr=3&upstream=4562&downstream=9042&rc=0&gstid=3 </blockquote> | ||
* | *; dsid | ||
: This is a [[dataset id]] for the sequence to be loaded. | |||
This is the [[chromosome]] from the dataset associated with the dataset id. | *; chr | ||
:This is the [[chromosome]] from the dataset associated with the dataset id. | |||
* upstream | *; 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. | |||
* downstream | |||
This represents the stop position of the sequence on the chromosome selected. | |||
=== Parameters Utilized In General === | === Parameters Utilized In General === | ||
* rc | *; 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. | |||
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'''' | *; gstid | ||
:''''TODO'''' | |||
Revision as of 22:11, 14 April 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'