I'm trying to do some programming with Tcl, Pregap and Gap.
At the moment my script is able to suggest primers for an assembly, write them into a file and tag the corresponding reads. Now I would like to know to which contig an tagged read belongs. But unfortunately I wasn't able to find a built-in function for this purpose.
Now I came up with this idea:
*get list of all contigs
*walk throug primer list and get reading_name
*walk throug all contigs until you find the reading_name
*goto next primer
But now I hit a new problem, how it is possible to check if my current viewed contig contains the searched reading? Is there a way to walk through the contig - list - structure to the contained reads?
Any kind of help or hints would be appreciated.
With kind regards,
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