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Importclonenames configuration

This configuration keyword defines the script or program which produces the clonenames for a given gel.

Clone names are required when the gel processing gets to step 3. They are either read from an existing names file or from an external script.
If either method fails, they are initialized depending on a default naming scheme and an initial template (See gel parameters "namingscheme" and first clone name ("nametemplate") ).

The external script which is configured by the keyword "importclonenames" will writes the clone names to STDOUT. The command is opened as a pipe and the names are read directly from the output of that program.

You probably need to configure to pass the parameters "projectname" and "gelname" as argument to that script. In some applications that script is an interactive Perl/TK interface, in other cases it run an oracle query against the lab's tracking database.

An example of a command line configuration of the $importclonenames keyword would be :

/usr/local/image/bin/cname $projectname $gelname

If you have written a local script or utility called cname in the given directory.

Input format

When you write the external clonenames tool it is important to understand how they are read by image.

There is one line for every sample lane. The lines are separated by the usual newline character (called \n in C or Perl). For a gel with lanenumber = 29 and markerrepeat = 7 you need to print out 24 lines (because the gel has 5 marker lanes).

If the gel doesn't need to store separate digests per clone, only one word per line is necessary. This word is the clonename.

If digests are used the line is split by the colon character ':'. Everything before the colon is treated as the clonename, everything after the colon is treated as the digest name for that lane.

By default every sample lane is switched on. The output of the clone-names script can also be used to switch off lanes that are already known not to be useful. If the first character in a line is a '#' character the lane will be switched off. A clone name can still be submitted after the '#', which may be useful if you decide to use the clone at a later date.

Special characters :

The input specifications suggest that there are two special characters, the hash-sign '#' and the colon ':'. If they are required anywhere in the clone or digest name they have to escaped with a backslash so they aren't mistaken for the character that switches a lane off or separates the clone from the digest name respectively.

Example output

A rather artificial example of the output shows how the the hash-character is handled when the names are read :

The example is the first 12 lines of output for a 24 clone gel (lanenumber = 29, markerrepeat = 7).

output line clonename digest lane # flag
\#abc\:A\:1:digest\:1 #abc:A:1 digest:1 lane 1 (on)
#abcA2\::digest2 abcA2: digest2 lane 2 (off)
\#abcA3:digest1: #abcA3 digest1: lane 3 (on)
#abcA4 abcA4   lane 4 (off)
##abcA5 #abcA5   lane 5 (off)
\#\#abcA6\#:digest:1 ##abcA6# digest1 lane 6 (on)
\##abcA7 ##abcA7   lane 8 (on)
# <empty>   lane 9 (off)
\# #   lane 10 (on)
ab\#cA10 ab#cA10   lane 11 (on)
ab#cA11 ab#cA11   lane 12 (on)
abcA12 abcA12   lane 13 (on)

Lane 1 shows how the hash and the colon character can be escaped so they are allowed in the clone/digest name. Lane 9 shows how the script could mark failed lanes - a simple hash on that line will switch the lane off and assign a blank clone/digest name.

Lane 5 and 8 show that only the first hash-sign in the line has to be escaped, hashes after that will not cause the lane to be switched off. Similarly lane 3 and 6 show that a colon in the digest name doesn't have to be escaped because the clone and digest were already split on the first colon in the line.

However it would be good practise to always escape the special characters : and #. This will ensure maximum forward compatibility. Maybe in the future a third field will be introduced for the colon separated input line, and missing escape-backslashes in the digest name would jeopardize such extensions.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/qg16xvjm