AGCoL
Arizona Genomics
Computational Laboratory
Tucson, AZ

WebFPC Site Manual
WebAGCoL | WebFPC User Manual | FPC

CONTENTS

  1. PREREQUISITES
  2. HOW WebFPC WORKS
  3. LINKING TO WebFPC FROM A REMOTE SITE
  4. FILE FORMATS & CONFIG
PREREQUISITES

Install Java 1.4.0_03
-- http://java.sun.com/products/archive/j2se/1.4.0_03/index.html

HOW WebFPC WORKS

WebFPC is written as a Java applet, and its class files are compressed into 'jar' files. A simple HTML file (i.e. index.html) references these jar files, and loads the applet into the web browser at the size specified in the HTML file. The applet retrieves files from the host server containing information on the contigs as they are needed, and uses the data in the files to display contig information in the applet window. These files are created from the FPC file via a perl script (webagcol_install/webfpc/splitter.pl). For each contig, a separate gzipped XML file is created in <PROJECT_DIRECTORY>/WebAGCoL/WebFPC/DATA/. The applet retrieves the information from this location for the contig that needs to be displayed. The Java implementation of the SAX parser is used by WebFPC to retrieve the contig's XML file while simultaneously parsing it.

Web References: The splitter.pl script looks in the <REFERENCES_DIR> for files that contain information on linking clones and/or markers to remote sites. A separate file must be created for each remote site to link to. The information retrieved from these files is written into the contig XML files. For the format of these files, see the File formats section.

LINKING TO WebFPC FROM A REMOTE SITE   Back to top

WebFPC allows external applications to intiate the contig display. To do so, the CGI script "WebFPC_Direct_v2.1.cgi" is called with the project name, and either a clone name or marker name or contig number. Note, all parameters are currently case sensitive.

Parameter Rule Value
name Required The name of the FPC project.
contig Either The index number of the contig. Note: Value must be an integer, i.e. do not prefix with 'ctg'.
clone Or The name of the clone that is to be selected.
marker Or The name of the marker that is to be selected.

Examples

For example, AGCoL'S URL is
http://www.genome.arizona.edu/cgi-bin/WebFPC/WebFPC_Direct_v2.1.cgi.

To display contig 14 in the rice project, append the following to the above url: ?name=rice&contig=14.

If you wish to display the contig containing clone a0025J10, append ?name=rice&&clone=a0025J10 .

If you wish to display the contig containing marker SOG1332, append ?name=rice&&marker=SOG1332. If the marker is contained in more than one contig, the list of contigs will be displayed

Project Parameter

The 'name' parameter must be in the config file as MAP_NAME. See Installing WebAGCoL for more information.

FILE FORMATS & CONFIG   Back to top

The following config variables are used: FPC_FILE, REFERENCE_DIR, SHOTGUN_COLORS, TYPE_COLORS.

All files in this section are put into the <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME> directory by the setup.pl script, and can later be changed by the user (the update.sh needs to be rerun after a change). This directory will be referred to as the MAP directory in the following discussion.

Reference file

One or more reference files are in the a directory specified by REFERENCE_DIR. The update.sh will create a sub-directory /references of the MAP directory, and move the reference files into it. Thereafter, you can update the directory yourself, and run update.sh so that WebFPC will have the new/modified links. The format for the input files:

<Site Name>
["Clone List:"<clone url prefix> [<clone url postfix>]
(<clone name in fpc file> [<clone name on site>])+|"all"
"end"]
["Marker List:"<marker url prefix> [<marker url postfix>]
(<marker name in fpc file> [<marker name on site>])+|"all"
"end"]

Example File:

Clone List:http://www.ncbi.nlm.nih.gov:80/entrex/query.fcgi?cmd=Search&term=&dopt=GenBank 
aDC1A0 DCPaDC1A0
aDC1B3 DCPaDC1B3
end

Marker List:http://www.ncbi.nlm.nih.gov:80/entrex/query.fcgi?cmd=Search&db=Probe&term=
all
end

Explanation of Example:

The site name is the name by which the site will be referred to by WebFPC.

The URL may have two parts: one that goes before the clone or marker identifier, and one that goes after it. The second one is optional. The two parts are separated by white space. An example clone url, for clone aDC1A0, from this list would be http://www.ncbi.nlm.nih.gov:80/entrex/query.fcgi?cmd=Search&db=Nucleotide&term=DCPaDC1A0&dopt=GenBank . Notice that the clone is referred to as aDC1A0 on the WebFPC screen, but DCPaDC1A0 is used to look it up on the web site.

If all clones in FPC are also in the remote site, and they use the same names, the word 'all' can be entered.

The marker list works the same as the clone list. However, it is used to link markers instead of clones.

Shotgun colors

An optional file, called 'shotgun_colors', is created in the /config sub-directory of the MAP directory by the upate.pl script. It is used to highlight clones with a sequencing status. The format is: 

<SHOTGUN TYPE> <COLOR>
An example, highlighting all clones with a SENT, FINISHED, or SHOTGUN status yellow, is given below: 
SENT blue
FINISHED yellow
SHOTGUN yellow
Listed below are all valid colors:
  • blue
  • dark_gray
  • gray
  • light_gray
  • magenta
  • orange
  • pink
  • red
  • yellow

Type colors

An optional file, called 'type_colors', is created by the /config sub-directory of the MAP directory by the update.sh script. It is used to highlight markers of a particular type. The format is: 

<MARKER TYPE> <COLOR>
An example, highlighting STS and eMRK clones yellow, is given below: 
STS yellow
eMRK yellow
The list of valid colors is the same as for the Shotgun colors.

Help URL   Back to top

A file containing the URL of the WebFPC User's Manual is placed in config directory by the setup.pl script. It is called 'help_url', and should not need to be modified, unless the documentation is moved.

Email comments to vishal@genome.arizona.edu