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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, caBIG-05Apr06-00, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
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# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
# This file is part of the SEED Toolkit.
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.


=head1 assign_towards_subsystems

This is a much more relaxed assignment algorithm that will suggest assignments to pegs from a genome provided that 
  (1) the new function is in a subsystem
  (2) the current peg is not in a subsystem
  (3) the current function does not tie this peg to any other subsystem (this is essentially the same as #2 although that could require refilling a spreadsheet)
  (4) the function does not currently exist in this genome (although that can be overriden), to avoid spurious paralogs

Use this command as follows:

assign_towards_subsystems [user=User] [not_unique] [maxN=] [maxP=] genome > relaxed_assignments.txt

Options need to be preceeded by their command. Assignments are not actually made, rather they are printed out for a subsequent auto assignment. This method particularly favors finding functions that are in subsystems.


use FIG;
use strict;

my $fig=new FIG;

my $usage="$0 [user=User] [not_unique] [maxN=] [maxP=] genome > relaxed_assignments.txt";

my $user="master:auto_assign";
my ($unique, $maxN, $maxP)=(1,50,1e-20);
my $genome=shift;
while ($genome && ($genome !~ /^\d+\.\d+$/))
 if ($genome eq "not_unique") {$unique=0}
 if ($genome =~ /user=(\S+)/) {$user=$1}
 if ($genome =~ /maxN=(\S+)/) {$maxN=$1}
 if ($genome =~ /maxP=(\S+)/) {$maxP=$1}

die $usage unless ($genome);
die "$genome is not a valid genome" unless ($fig->genus_species($genome));

print STDERR "PARAMETERS:\nUNIQUE: $unique\nUser: $user\nMaxN: $maxN\nMaxP: $maxP\nGenome: $genome\n";

# find out what else is in subsystems
my $known_ss; # roles of things that are in ss
map {$known_ss->{$_->[1]}=1} $fig->subsystems_roles;

# find out the current annotations and whether that annotation would 
# associate the peg with a subsystem
my $fns; my $in_ss;
map {
 my $peg=$_;
 my $fn=scalar($fig->function_of($peg));
 ($known_ss->{$fn}) ? ($in_ss->{$peg}=1) : 1;
} $fig->pegs_of($genome);

# work through the sims
foreach my $peg ($fig->pegs_of($genome))
 # the figx here expands the sims to include all fig ids.
 next if ($in_ss->{$peg});
 foreach my $sim ($fig->sims($peg, $maxN, $maxP, 'figx'))
  my $fn=scalar($fig->function_of($sim->[1]));
  next unless ($known_ss->{$fn}); # this role is not in a subsystem
  next if ($unique && $fns->{$fn}); # we have already seen this function
  print "$peg\t$fn\n";

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