[Bioperl-l] AGI's fpc stuff: Bio::Map::Physical, Bio::MapIO::fpc, etc

Robert Buels rmb32 at cornell.edu
Tue Dec 15 10:09:43 EST 2009

Hi all,

Recently I caught an interesting thing related to making GFF files out
of FPC maps built recently using Bio::MapIO;:fpc.  All of the 
coordinates in the resulting GFF3 and the sizes of the contigs and 
clones seem to be dilated by 4x from where they should be.

This didn't happen with some earlier FPC datasets I ran through these 

I haven't gone through any of this very thoroughly, but I notice in 
Bio::Map::Physical::print_gffstyle() at line 765 there's a line like 'my 
$basepair = 4096', and the routine goes on to use $basepair as a sort of 
multiplier for converting the native physical map units into basepairs 
for GFF-style output.

This makes me wonder if the newer FPC datasets coming out require a 
different $basepairs value, maybe 1024?  Are the original authors of 
these modules still around on this list?


Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu

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