#!/usr/bin/perl -w =head1 GenomeFile This script generates a genome file. The file will include all complete genomes except the ones listed as parameters. The currently-supported command-line options are as follows. =over 4 =item user Name suffix to be used for log files. If omitted, the PID is used. =item trace Numeric trace level. A higher trace level causes more messages to appear. The default trace level is 2. Tracing will be directly to the standard output as well as to a CIC<.log> file in the FIG temporary directory, where I is the value of the B option above. =item sql If specified, turns on tracing of SQL activity. =item background Save the standard and error output to files. The files will be created in the FIG temporary directory and will be named CIC<.log> and CIC<.log>, respectively, where I is the value of the B option above. =item h Display this command's parameters and options. =item phone Phone number to message when the script is complete. =item geneFile Name of the gene file to produce. The default is C in the SproutData directory. =item code Access code to assign to the genomes. =back =cut use strict; use Tracer; use DocUtils; use TestUtils; use Cwd; use File::Copy; use File::Path; use FIG; # Get the command-line options and parameters. my ($options, @parameters) = StandardSetup([qw() ], { phone => ["", "phone number (international format) to call when load finishes"], code => ["1", "genome access code"], geneFile => ["$FIG_Config::sproutData/genes.tbl", "output file"], }, " ...", @ARGV); # Set a variable to contain return type information. my $rtype; # Insure we catch errors. eval { my $fig = FIG->new(); # Get the access code. my $code = $options->{code}; # Get a list of the complete genomes. my @genes = $fig->genomes(1); # Start a counter. my $counter = 0; # Open the output file. my $outFile = $options->{geneFile}; Open(\*GENEFILE, ">$outFile"); # Loop through the genes, creating output. for my $gene (@genes) { # Check to see if this gene is being excluded. if (grep { $_ eq $gene } @parameters) { Trace("Genome $gene excluded.") if T(3); } else { print GENEFILE "$gene\t$code\n"; $counter++; } } # Close the output file. close GENEFILE; Trace("$counter genomes written to $outFile.") if T(2); }; if ($@) { Trace("Script failed with error: $@") if T(0); $rtype = "error"; } else { Trace("Script complete.") if T(2); $rtype = "no error"; } if ($options->{phone}) { my $msgID = Tracer::SendSMS($options->{phone}, "GenomeFile terminated with $rtype."); if ($msgID) { Trace("Phone message sent with ID $msgID.") if T(2); } else { Trace("Phone message not sent.") if T(2); } } 1;