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Special List Names

Some lists are automatically updated or are generated on-the-fly as needed. The lists named "contigs" and "readings" correspond to the currently selected contigs in the contig selector window and the currently selected readings in the template displays. Note that lists (with any names) can also be created from selected items in the contig editor.See section Set Output List. The "allcontigs" and "allreadings" lists are created as needed and always contain an identifier for every contig and every reading identifier.

Using a list name consisting of a contig identifier surrounded by square brackets ('[' and ']') will create and use a list containing all of the readings within that contig. For example, to extract all the readings from contig 'xb54f8.s1', the list name given in Extract Readings would be '[xb54f8.s1]'.

Surrounding a list name with curly brackets ('{' and '}') will create a use a list containing all of the readings within the contigs named within the specified list name. So '{contigs}' expands to all the readings within the contigs contained in the 'contigs' list. Hence the 'allreadings' list is identical to '{allcontigs}'.

These list can be used anywhere where a list name is required except for editing and deletion of lists. So to produce a file of filenames from the currently selected contigs it is possible to save the list named '{contigs}' to a file.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_127.html