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Revision 1.1 - (view) (download) (as text)
| 1 : | redwards | 1.1 | #__perl__ |
| 2 : | |||
| 3 : | use strict; | ||
| 4 : | use Data::Dumper; | ||
| 5 : | use FIG; | ||
| 6 : | my $fig = new FIG; | ||
| 7 : | use Getopt::Std; | ||
| 8 : | my %opts; | ||
| 9 : | getopts('sg:a', \%opts); | ||
| 10 : | |||
| 11 : | die <<EOF unless ($opts{g}); | ||
| 12 : | $0 | ||
| 13 : | -g genome id | ||
| 14 : | -a make the annotations (otherwise just print them out) | ||
| 15 : | -s don't print things out - just make the annotations | ||
| 16 : | |||
| 17 : | EOF | ||
| 18 : | |||
| 19 : | |||
| 20 : | foreach my $peg ($fig->pegs_of($opts{g})) { | ||
| 21 : | my @tuples = $fig->subsystems_for_peg($peg); | ||
| 22 : | next if (scalar(@tuples)); # ignore any protein aleady in a subsystem | ||
| 23 : | |||
| 24 : | my $ss; my $count; | ||
| 25 : | foreach my $sim ($fig->sims($peg, 500, 1e-3, 'figx')) { | ||
| 26 : | my $opeg = $sim->[0]; | ||
| 27 : | ($opeg eq $peg) ? ($opeg = $sim->[1]) : 1; | ||
| 28 : | foreach my $tuple ($fig->subsystems_for_peg($opeg)) { | ||
| 29 : | my ($subsys, $fn, $vc)=@$tuple; | ||
| 30 : | push @{$ss->{$fn}}, $subsys if ($fig->usable_subsystem($subsys, 1)); | ||
| 31 : | $count->{$fn}++; | ||
| 32 : | } | ||
| 33 : | } | ||
| 34 : | |||
| 35 : | next unless (scalar(keys %$ss)); | ||
| 36 : | |||
| 37 : | my $thisfn = scalar($fig->function_of($peg)); | ||
| 38 : | if ($ss->{$thisfn}) { | ||
| 39 : | (!$opts{s}) && map {print join("\t", $peg, $thisfn, $thisfn, $_), "\n"} @{$ss->{$thisfn}}; | ||
| 40 : | } | ||
| 41 : | else { | ||
| 42 : | my @abundant = sort {$count->{$b} <=> $count->{$a}} keys %$count; | ||
| 43 : | (!$opts{s}) && map {print join("\t", $peg, $thisfn, $abundant[0], $_), "\n"} @{$ss->{$abundant[0]}}; | ||
| 44 : | if ($opts{a}) { | ||
| 45 : | $fig->assign_function($peg, "AutoUpdate", $abundant[0]); | ||
| 46 : | } | ||
| 47 : | } | ||
| 48 : | } | ||
| 49 : | |||
| 50 : | |||
| 51 : |
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