This is the command substitch.pl that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
substitch.pl -- Split/merge stitch files into/out of stitch files
SYNOPSIS
substitch.pl --split 5 allchromosomes.stitch #split big stitch into 5 roughly equal
chunks
substitch.pl --project allspecies.seqs sub.anchors #project some anchors into a different
coordinate space (as long as the stitch component sequences match)
OPTIONS
--verbose => makes more verbose --faketfidf => fake tfidf scores based on score stat in
file
Note on split: This program does not claim to produce an optimal splitting. It tries a
couple heuristics, refines the results, and picks the best arrangement it's found so far.
Technically this is a variation on the traditional "trunk packing problem," which is (at
least in the abstract case) NP-hard, if I remember 15-251 correctly. This particular
variety of trunk packing however, seems like it should be solvable faster (worst case some
n^k dynamic programming I think, but I'm betting this way is faster and tons easier to
write for 90% of the cases out there). If anyone reading this goes "You moron, this has
been solved a thousand times already," please let me know how: [email protected]
Use substitch.pl online using onworks.net services
