Keith Robison writes:
> I've been trying to use Pretty to format some alignments, and seem
> to have run into a limit of 110 residues per line. Has anyone else
> experienced this? This limit does not appear to be documented.
If you look in the GCG source file GenSource:Pretty.For, in the code
for the Subroutine PrettyOut, you will see a statement restricting
the variable LineSize's value (changeable from the default 50 via
command-line option) to the range [1,110]:
LineSize = CLRetInt('LINesize', 1, 110, LineSize)
I'll guess that the program authors assumed most users would never
choose to generate an output file containing lines longer than 132
characters, and they chose the 110 limit to allow sufficient space
at the beginning of lines to accommodate reasonably long sequence
identifiers. Yes, that limit does not seem to be documented outside
the code itself.
In that same section of code, it looks to me as if the character
array used for assembling lines of Pretty'd sequence output is
declared large enough to hold about 256 characters. In principle,
you could change the Pretty source code, raising the LineSize upper
limit to a value somewhat higher than 110, recompile, relink, and
rerun. However, without studying the full Pretty code carefully for
delicate dependencies, it probably makes sense to ask the GCG folks
about it first.
Mark Reboul
Columbia-Presbyterian Cancer Center Computing Facility
mark at cuccfa.ccc.columbia.edu
