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The lanes file

The lanes are computed by the lanetracking program and the data is written in shape of a grid. An evenly spaced set of points for each lane that describes a line running horizontally (after image rotation) across the lanes. This map of lane-points is displayed in the lanetracking-editor in Step 2.

File format

The lane grid for every gel is stored in a file called "lanes" in the gel-directory.

The first line of the file contains the word "LANES".

The whole gel is divided up horizontally into evenly spaced zones. The intersection of the lane with a zone boundary is marked with a vertical coordinate. The number of zones is set with the "zonenumber" parameter in the gel parameter dialog. The lanes file contains one line per zone boundary, so following the line with the word LANES, there are zonenumber + 1 lines in the file. One could think of a set of combs where lines that connect up corresponding teeth make up the lane-map. The more combs, the more accurate the curvature of the lanes can be followed. The minimum number of combs of obviously 2, which describes straight lines from the well to the end of the gel, which won't be very use at all.

Each line specifies which zone it belongs to and where the zone is horizontally located along the gel. Following that there is one floating-point value for each lane describing the vertical coordinate at which the lane intersects the zones edge. The "lanenumber" parameter describes how many such numbers there are per zone.

Each line has therefore lanenumber + 2 elements :

z=zone-counter x=zone-position lane-y0 lane-y1 ...

So the 4th lane-y floating point number describes a point for lane number 3 (the first lane has number 0). These values are sorted in descending numerical order, because the first lane is drawn along the bottom of the rotated gel (i.e. with the largets y-coordinates).

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/v5g14gfo