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Annotation of /FigKernelScripts/ma_pipeline.pl

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1 : overbeek 1.1 use strict;
2 :     use Data::Dumper;
3 :    
4 :     my $usage = "usage: ma_pipeline OrgDir";
5 :    
6 :     my($orgD);
7 :     (
8 :     ($orgD = shift @ARGV)
9 :     )
10 :     || die $usage;
11 :    
12 :     my $exp_ed = "$orgD/UserSpace/ExpressionData";
13 :     (-d $exp_ed)
14 :     || die "Where is $exp_ed?";
15 :     (-s "$exp_ed/probes")
16 :     || die "Where is $exp_ed/probes?";
17 :     (-s "$orgD/contigs")
18 :     || die "Where is $orgD/contigs?";
19 :     (-s "$orgD/Features/peg/tbl")
20 :     || die "Where is $orgD/Features/peg/tbl?";
21 :    
22 :     system "make_probes_to_genes $exp_ed/probes $orgD/contigs $orgD/Features/peg/tbl $exp_ed/peg.probe.table $exp_ed/probe.occ.table 2> $exp_ed/problems";

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