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Revision 1.15 - (view) (download) (as text)
| 1 : | overbeek | 1.1 | use strict; |
| 2 : | use Data::Dumper; | ||
| 3 : | |||
| 4 : | overbeek | 1.15 | my $usage = "usage: ma_pipeline Genome"; |
| 5 : | overbeek | 1.1 | |
| 6 : | overbeek | 1.3 | my($genome,$orgD); |
| 7 : | overbeek | 1.1 | ( |
| 8 : | overbeek | 1.3 | ($genome = shift @ARGV) && ($orgD = "$FIG_Config::organisms/$genome") |
| 9 : | overbeek | 1.1 | ) |
| 10 : | || die $usage; | ||
| 11 : | overbeek | 1.3 | |
| 12 : | (-d $orgD) || die "invalid organism directory"; | ||
| 13 : | |||
| 14 : | overbeek | 1.15 | # (my $rma_key = shift @ARGV) |
| 15 : | # || die $usage; | ||
| 16 : | overbeek | 1.1 | |
| 17 : | my $exp_ed = "$orgD/UserSpace/ExpressionData"; | ||
| 18 : | (-d $exp_ed) | ||
| 19 : | || die "Where is $exp_ed?"; | ||
| 20 : | (-s "$exp_ed/probes") | ||
| 21 : | || die "Where is $exp_ed/probes?"; | ||
| 22 : | (-s "$orgD/contigs") | ||
| 23 : | || die "Where is $orgD/contigs?"; | ||
| 24 : | (-s "$orgD/Features/peg/tbl") | ||
| 25 : | || die "Where is $orgD/Features/peg/tbl?"; | ||
| 26 : | |||
| 27 : | overbeek | 1.11 | my $tbl = (-s "$exp_ed/tbl") ? "$exp_ed/tbl" : "$orgD/Features/peg/tbl"; |
| 28 : | overbeek | 1.10 | &run("make_probes_to_genes $exp_ed/probes $orgD/contigs $tbl $exp_ed/peg.probe.table $exp_ed/probe.occ.table 2> $exp_ed/problems"); |
| 29 : | overbeek | 1.4 | &run("remove_multiple_occurring_probes $exp_ed/peg.probe.table $exp_ed/probe.occ.table > $exp_ed/peg.probe.table.no.multiple"); |
| 30 : | overbeek | 1.3 | chdir $exp_ed; |
| 31 : | |||
| 32 : | olson | 1.12 | my $peg_probe_table = "$exp_ed/peg.probe.table.no.multiple"; |
| 33 : | my $probe_no_match = "$exp_ed/probe.no.match"; | ||
| 34 : | |||
| 35 : | &make_missing_probes($peg_probe_table, "$exp_ed/probes", $probe_no_match); | ||
| 36 : | |||
| 37 : | &run("Rscript $FIG_Config::bin/RunRMA.R $peg_probe_table $probe_no_match $exp_ed/Experiments $exp_ed 2> $exp_ed/stderr.RMA"); | ||
| 38 : | |||
| 39 : | overbeek | 1.15 | # &run("Rscript $FIG_Config::bin/RunRMA.R $rma_key $exp_ed $exp_ed/Experiments 2> $exp_ed/stderr.RMA"); |
| 40 : | overbeek | 1.9 | |
| 41 : | overbeek | 1.3 | &run("$FIG_Config::bin/call_coregulated_clusters_on_chromosome $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.clusters 2> $exp_ed/stderr.coregulated.clusters"); |
| 42 : | &run("$FIG_Config::bin/make_coreg_conjectures_based_on_subsys $genome $exp_ed/raw_data.tab > $exp_ed/coregulated.subsys 2> $exp_ed/stderr.coregulated.subsys"); | ||
| 43 : | overbeek | 1.7 | &run("cat $exp_ed/coregulated.clusters $exp_ed/coregulated.subsys | cut -f1 | $FIG_Config::bin/merge_gene_sets | filter_on_known $exp_ed/raw_data.tab > $exp_ed/merged.clusters"); |
| 44 : | overbeek | 1.5 | |
| 45 : | overbeek | 1.7 | &run("get_ON_probes $genome $exp_ed/probe.occ.table $exp_ed/peg.probe.table $exp_ed/raw_data.tab > $exp_ed/probes.always.on"); |
| 46 : | overbeek | 1.8 | &run("cut -f2 $exp_ed/probes.always.on | sort -u > $exp_ed/pegs.always.on"); |
| 47 : | overbeek | 1.6 | &run("Rscript $FIG_Config::bin/Pipeline.R $exp_ed/pegs.always.on $exp_ed/merged.clusters > $exp_ed/comments.by.Pipeline.R"); |
| 48 : | overbeek | 1.13 | |
| 49 : | overbeek | 1.14 | &run("Rscript $FIG_Config::bin/SplitGeneSets.R $exp_ed/merged.clusters 0.7 > $exp_ed/split.clusters"); |
| 50 : | overbeek | 1.9 | |
| 51 : | sub make_missing_probes | ||
| 52 : | { | ||
| 53 : | my($probe_table, $probes, $output) = @_; | ||
| 54 : | open(MATCH,"<", $probe_table) or die "Cannot open $probe_table: $!"; | ||
| 55 : | open(PROBES,"<", $probes) or die "Cannot open $probes: $!"; | ||
| 56 : | open(OUTPUT, ">", $output) or die "Cannot open $output: $!"; | ||
| 57 : | my %locations; | ||
| 58 : | while(<MATCH>) | ||
| 59 : | { | ||
| 60 : | chomp; | ||
| 61 : | my($peg,$loc)=split "\t"; | ||
| 62 : | $locations{$loc} = $peg; | ||
| 63 : | } | ||
| 64 : | |||
| 65 : | while(<PROBES>) | ||
| 66 : | { | ||
| 67 : | chomp; | ||
| 68 : | my($loc,$seq) = split "\t"; | ||
| 69 : | print OUTPUT $loc, "\n" if ! exists $locations{$loc}; | ||
| 70 : | } | ||
| 71 : | close(MATCH); | ||
| 72 : | close(PROBES); | ||
| 73 : | close(OUTPUT); | ||
| 74 : | } | ||
| 75 : | overbeek | 1.3 | |
| 76 : | sub run { | ||
| 77 : | shift if UNIVERSAL::isa($_[0],__PACKAGE__); | ||
| 78 : | my($cmd) = @_; | ||
| 79 : | overbeek | 1.2 | |
| 80 : | overbeek | 1.3 | if ($ENV{FIG_VERBOSE}) { |
| 81 : | my @tmp = `date`; | ||
| 82 : | chomp @tmp; | ||
| 83 : | print STDERR "$tmp[0]: running $cmd\n"; | ||
| 84 : | } | ||
| 85 : | (system($cmd) == 0) || die("FAILED: $cmd"); | ||
| 86 : | } | ||
| 87 : | overbeek | 1.2 |
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