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| 1 : | efrank | 1.1 | # -*- perl -*- |
| 2 : | olson | 1.2 | # |
| 3 : | # Copyright (c) 2003-2006 University of Chicago and Fellowship | ||
| 4 : | # for Interpretations of Genomes. All Rights Reserved. | ||
| 5 : | # | ||
| 6 : | # This file is part of the SEED Toolkit. | ||
| 7 : | # | ||
| 8 : | # The SEED Toolkit is free software. You can redistribute | ||
| 9 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 10 : | # Public License. | ||
| 11 : | # | ||
| 12 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 13 : | # along with this program; if not write to the University of Chicago | ||
| 14 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 15 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 16 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 17 : | # | ||
| 18 : | |||
| 19 : | efrank | 1.1 | |
| 20 : | use Carp; | ||
| 21 : | use Data::Dumper; | ||
| 22 : | use FIG; | ||
| 23 : | |||
| 24 : | my $fig = new FIG; | ||
| 25 : | $| = 1; | ||
| 26 : | |||
| 27 : | # usage: make_occ_counts CutOff > counts | ||
| 28 : | |||
| 29 : | ( $cutoff = shift @ARGV) | ||
| 30 : | || die "usage: make_occ_counts CutOff > counts"; | ||
| 31 : | |||
| 32 : | opendir(SIMS,"$FIG_Config::data/Sims") || die "could not open Sims"; | ||
| 33 : | @files = grep { $_ !~ /^\./ } readdir(SIMS); | ||
| 34 : | closedir(SIMS); | ||
| 35 : | |||
| 36 : | foreach $file (@files) | ||
| 37 : | { | ||
| 38 : | &process("$FIG_Config::data/Sims/$file"); | ||
| 39 : | } | ||
| 40 : | |||
| 41 : | sub process { | ||
| 42 : | my($file) = @_; | ||
| 43 : | my(%seen,$x,$curr,$count); | ||
| 44 : | |||
| 45 : | open(TMP,"<$file") || die "could not open $file"; | ||
| 46 : | |||
| 47 : | if (defined($x = <TMP>)) | ||
| 48 : | { | ||
| 49 : | chop $x; | ||
| 50 : | $x = [split(/\t/,$x)]; | ||
| 51 : | } | ||
| 52 : | while (defined($x)) | ||
| 53 : | { | ||
| 54 : | $curr = $x->[0]; | ||
| 55 : | $count = 0; | ||
| 56 : | undef %seen; | ||
| 57 : | while (defined($x) && ($x->[0] eq $curr)) | ||
| 58 : | { | ||
| 59 : | if ((! $seen{$x->[1]}) && ($x->[10] <= $cutoff)) | ||
| 60 : | { | ||
| 61 : | $seen{$x->[1]} = 1; | ||
| 62 : | $count++; | ||
| 63 : | } | ||
| 64 : | |||
| 65 : | if (defined($x = <TMP>)) | ||
| 66 : | { | ||
| 67 : | chop $x; | ||
| 68 : | $x = [split(/\t/,$x)]; | ||
| 69 : | } | ||
| 70 : | } | ||
| 71 : | print "$count\t$curr\n"; | ||
| 72 : | } | ||
| 73 : | close(TMP); | ||
| 74 : | } | ||
| 75 : | |||
| 76 : | undef $fig; |
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